Perl modules on hebrides as of 30 January 2004 generated from pmdesc.pl ======================== Cwd (2.12) - get pathname of current working directory lib (0.5565) - manipulate @INC at compile time re (0.04) - Perl pragma to alter regular expression behaviour XSLoader (0.02) - Dynamically load C libraries into Perl code DynaLoader (1.04) - Dynamically load C libraries into Perl code B (1.02) - The Perl Compiler O (1.00) - Generic interface to Perl Compiler backends ByteLoader (0.05) - load byte compiled perl code DB_File (1.808) - Perl5 access to Berkeley DB version 1.x Encode (1.99) - character encodings encoding (1.48) - allows you to write your script in non-ascii or non-utf8 Fcntl (1.05) - load the C Fcntl.h defines IO (1.21) - load various IO modules NDBM_File (1.05) - Tied access to ndbm files ODBM_File (1.04) - Tied access to odbm files Safe (2.10) - Compile and execute code in restricted compartments Opcode (1.05) - Disable named opcodes when compiling perl code ops (1.00) - Perl pragma to restrict unsafe operations when compiling SDBM_File (1.04) - Tied access to sdbm files Socket (1.76) - load the C socket.h defines and structure manipulators Storable (2.09) - persistence for Perl data structures attrs (1.01) - set/get attributes of a subroutine (deprecated) threads (1.01) - Perl extension allowing use of interpreter based threads from perl Errno (1.09) - System errno constants Devel::DProf - a Perl code profiler Devel::PPPort (2.011) - Perl/Pollution/Portability Devel::Peek (1.01) - A data debugging tool for the XS programmer Digest::MD5 (2.33) - Perl interface to the MD5 Algorithm File::Glob (1.02) - Perl extension for BSD glob routine Filter::Util::Call (1.0601) - Perl Source Filter Utility Module I18N::Langinfo (0.02) - query locale information IPC::Msg (1.02) - SysV Msg IPC object class IPC::Semaphore (1.02) - SysV Semaphore IPC object class IPC::SysV (1.04) - SysV IPC constants PerlIO::encoding (0.07) - encoding layer PerlIO::scalar (0.02) - in-memory IO, scalar IO PerlIO::via (0.02) - Helper class for PerlIO layers implemented in perl Time::HiRes (1.52) - High resolution alarm, sleep, gettimeofday, interval timers Unicode::Normalize (0.28) - Unicode Normalization Forms B::Stash (-umain,-uutf8,-uattributes,-uRegexp,-uPerlIO,-uPerlIO::Layer,-uInternals,-uDB 1.00) - show what stashes are loaded B::Asmdata (1.01) - Autogenerated data about Perl ops, used to generate bytecode B::C - Perl compiler's C backend B::Deparse (0.64) - Perl compiler backend to produce perl code B::Debug (1.01) - Walk Perl syntax tree, printing debug info about ops B::Bblock (1.02) - Walk basic blocks B::Assembler (0.06) - Assemble Perl bytecode B::Terse (1.02) - Walk Perl syntax tree, printing terse info about ops B::CC (1.00) - Perl compiler's optimized C translation backend B::Concise (0.56) - Walk Perl syntax tree, printing concise info about ops B::Lint (1.02) - Perl lint B::Showlex (1.00) - Show lexical variables used in functions or files B::Bytecode (1.01) - Perl compiler's bytecode backend B::Disassembler - Disassemble Perl bytecode B::Xref (1.01) - Generates cross reference reports for Perl programs B::Stackobj (1.00) - Helper module for CC backend Data::Dumper (2.121) - stringified perl data structures, suitable for both printing and C Encode::Alias (1.38) - alias definitions to encodings Encode::Encoding (1.33) - Encode Implementation Base Class Encode::Guess (1.09) - Guesses encoding from data Encode::Config (1.07) - internally used by Encode Encode::Encoder (0.07) - Object Oriented Encoder Encode::CJKConstants (1.02) - Internally used by Encode::??::ISO_2022_* Encode::Byte (1.23) - Single Byte Encodings Encode::CN (1.24) - China-based Chinese Encodings Encode::EBCDIC (1.21) - EBCDIC Encodings Encode::JP (1.25) - Japanese Encodings Encode::KR (1.23) - Korean Encodings Encode::Symbol (1.22) - Symbol Encodings Encode::TW (1.26) - Taiwan-based Chinese Encodings Encode::Unicode (1.40) - Various Unicode Transformation Formats IO::Pipe (1.122) - supply object methods for pipes IO::File (1.10) - supply object methods for filehandles IO::Select (1.16) - OO interface to the select system call IO::Socket (1.28) - Object interface to socket communications IO::Poll (0.06) - Object interface to system poll call IO::Dir (1.04) - supply object methods for directory handles IO::Handle (1.23) - supply object methods for I/O handles IO::Seekable (1.09) - supply seek based methods for I/O objects MIME::QuotedPrint (2.21) - Encoding and decoding of quoted-printable strings MIME::Base64 (2.21) - Encoding and decoding of base64 strings Sys::Hostname (1.11) - Try every conceivable way to get hostname Sys::Syslog (0.04) - Perl interface to the UNIX syslog(3) calls XS::APItest (0.03) - Test the perl C API XS::Typemap (0.01) - module to test the XS typemaps distributed with perl threads::shared (0.92) - Perl extension for sharing data structures between threads AnyDBM_File (1.00) - provide framework for multiple DBMs attributes (0.06) - get/set subroutine or variable attributes AutoLoader (5.60) - load subroutines only on demand AutoSplit (1.04) - split a package for autoloading autouse (1.03) - postpone load of modules until a function is used base (2.04) - Establish IS-A relationship with base classes at compile time Benchmark (1.052) - benchmark running times of Perl code bigint (0.04) - Transparent BigInteger support for Perl bignum (0.14) - Transparent BigNumber support for Perl bigrat (0.06) - Transparent BigNumber/BigRational support for Perl blib (1.02) - Use MakeMaker's uninstalled version of a package bytes (1.01) - Perl pragma to force byte semantics rather than character semantics Carp (1.01) - warn of errors (from perspective of caller) CGI (3.01) - Simple Common Gateway Interface Class charnames (1.02) - define character names for C<\N{named}> string literal escapes constant (1.04) - Perl pragma to declare constants DB (1.0) - programmatic interface to the Perl debugging API (draft, subject to change) diagnostics (1.12) - produce verbose warning diagnostics Digest (1.05) - Modules that calculate message digests DirHandle (1.00) - supply object methods for directory handles Dumpvalue (1.11) - provides screen dump of Perl data. English (1.01) - use nice English (or awk) names for ugly punctuation variables Env (1.00) - perl module that imports environment variables as scalars or arrays Exporter (5.57) - Implements default import method for modules Fatal (1.03) - replace functions with equivalents which succeed or die fields (2.03) - compile-time class fields FileCache (1.03) - keep more files open than the system permits FileHandle (2.01) - supply object methods for filehandles filetest (1.01) - Perl pragma to control the filetest permission operators FindBin (1.44) - Locate directory of original perl script if (0.03) - C a Perl module if a condition holds integer (1.00) - Perl pragma to use integer arithmetic instead of floating point less (0.01) - perl pragma to request less of something from the compiler locale (1.00) - Perl pragma to use and avoid POSIX locales for built-in operations Memoize (1.01) - Make functions faster by trading space for time NEXT (0.60) - Provide a pseudo-class NEXT (et al) that allows method redispatch open (1.02) - perl pragma to set default PerlIO layers for input and output overload (1.01) - Package for overloading perl operations PerlIO (1.03) - On demand loader for PerlIO layers and root of PerlIO::* name space SelectSaver (1.00) - save and restore selected file handle SelfLoader (1.0904) - load functions only on demand Shell (0.5) - run shell commands transparently within perl sigtrap (1.02) - Perl pragma to enable simple signal handling sort (1.02) - perl pragma to control sort() behaviour strict (1.03) - Perl pragma to restrict unsafe constructs subs (1.00) - Perl pragma to predeclare sub names Switch (2.10) - A switch statement for Perl Symbol (1.05) - manipulate Perl symbols and their names Test (1.24) - provides a simple framework for writing test scripts Thread (2.00) - manipulate threads in Perl (for old code only) UNIVERSAL (1.01) - base class for ALL classes (blessed references) utf8 (1.02) - Perl pragma to enable/disable UTF-8 (or UTF-EBCDIC) in source code vars (1.01) - Perl pragma to predeclare global variable names (obsolete) vmsish (1.01) - Perl pragma to control VMS-specific language features warnings (1.03) - Perl pragma to control optional warnings sun4-solaris-thread-multi::Cwd - get pathname of current working directory sun4-solaris-thread-multi::lib - manipulate @INC at compile time sun4-solaris-thread-multi::re - Perl pragma to alter regular expression behaviour sun4-solaris-thread-multi::XSLoader - Dynamically load C libraries into Perl code sun4-solaris-thread-multi::DynaLoader - Dynamically load C libraries into Perl code sun4-solaris-thread-multi::B - The Perl Compiler sun4-solaris-thread-multi::O - Generic interface to Perl Compiler backends sun4-solaris-thread-multi::ByteLoader - load byte compiled perl code sun4-solaris-thread-multi::DB_File - Perl5 access to Berkeley DB version 1.x sun4-solaris-thread-multi::Encode - character encodings sun4-solaris-thread-multi::encoding - allows you to write your script in non-ascii or non-utf8 sun4-solaris-thread-multi::Fcntl - load the C Fcntl.h defines sun4-solaris-thread-multi::IO - load various IO modules sun4-solaris-thread-multi::NDBM_File - Tied access to ndbm files sun4-solaris-thread-multi::ODBM_File - Tied access to odbm files sun4-solaris-thread-multi::Safe - Compile and execute code in restricted compartments sun4-solaris-thread-multi::Opcode - Disable named opcodes when compiling perl code sun4-solaris-thread-multi::ops - Perl pragma to restrict unsafe operations when compiling sun4-solaris-thread-multi::SDBM_File - Tied access to sdbm files sun4-solaris-thread-multi::Socket - load the C socket.h defines and structure manipulators sun4-solaris-thread-multi::Storable - persistence for Perl data structures sun4-solaris-thread-multi::attrs - set/get attributes of a subroutine (deprecated) sun4-solaris-thread-multi::threads - Perl extension allowing use of interpreter based threads from perl sun4-solaris-thread-multi::Errno - System errno constants sun4-solaris-thread-multi::Devel::DProf - a Perl code profiler sun4-solaris-thread-multi::Devel::PPPort - Perl/Pollution/Portability sun4-solaris-thread-multi::Devel::Peek - A data debugging tool for the XS programmer sun4-solaris-thread-multi::Digest::MD5 - Perl interface to the MD5 Algorithm sun4-solaris-thread-multi::File::Glob - Perl extension for BSD glob routine sun4-solaris-thread-multi::Filter::Util::Call - Perl Source Filter Utility Module sun4-solaris-thread-multi::I18N::Langinfo - query locale information sun4-solaris-thread-multi::IPC::Msg - SysV Msg IPC object class sun4-solaris-thread-multi::IPC::Semaphore - SysV Semaphore IPC object class sun4-solaris-thread-multi::IPC::SysV - SysV IPC constants sun4-solaris-thread-multi::PerlIO::encoding - encoding layer sun4-solaris-thread-multi::PerlIO::scalar - in-memory IO, scalar IO sun4-solaris-thread-multi::PerlIO::via - Helper class for PerlIO layers implemented in perl sun4-solaris-thread-multi::Time::HiRes - High resolution alarm, sleep, gettimeofday, interval timers sun4-solaris-thread-multi::Unicode::Normalize - Unicode Normalization Forms sun4-solaris-thread-multi::B::Stash - show what stashes are loaded sun4-solaris-thread-multi::B::Asmdata - Autogenerated data about Perl ops, used to generate bytecode sun4-solaris-thread-multi::B::C - Perl compiler's C backend sun4-solaris-thread-multi::B::Deparse - Perl compiler backend to produce perl code sun4-solaris-thread-multi::B::Debug - Walk Perl syntax tree, printing debug info about ops sun4-solaris-thread-multi::B::Bblock - Walk basic blocks sun4-solaris-thread-multi::B::Assembler - Assemble Perl bytecode sun4-solaris-thread-multi::B::Terse - Walk Perl syntax tree, printing terse info about ops sun4-solaris-thread-multi::B::CC - Perl compiler's optimized C translation backend sun4-solaris-thread-multi::B::Concise - Walk Perl syntax tree, printing concise info about ops sun4-solaris-thread-multi::B::Lint - Perl lint sun4-solaris-thread-multi::B::Showlex - Show lexical variables used in functions or files sun4-solaris-thread-multi::B::Bytecode - Perl compiler's bytecode backend sun4-solaris-thread-multi::B::Disassembler - Disassemble Perl bytecode sun4-solaris-thread-multi::B::Xref - Generates cross reference reports for Perl programs sun4-solaris-thread-multi::B::Stackobj - Helper module for CC backend sun4-solaris-thread-multi::Data::Dumper - stringified perl data structures, suitable for both printing and C sun4-solaris-thread-multi::Encode::Alias - alias definitions to encodings sun4-solaris-thread-multi::Encode::Encoding - Encode Implementation Base Class sun4-solaris-thread-multi::Encode::Guess - Guesses encoding from data sun4-solaris-thread-multi::Encode::Config - internally used by Encode sun4-solaris-thread-multi::Encode::Encoder - Object Oriented Encoder sun4-solaris-thread-multi::Encode::CJKConstants - Internally used by Encode::??::ISO_2022_* sun4-solaris-thread-multi::Encode::Byte - Single Byte Encodings sun4-solaris-thread-multi::Encode::CN - China-based Chinese Encodings sun4-solaris-thread-multi::Encode::EBCDIC - EBCDIC Encodings sun4-solaris-thread-multi::Encode::JP - Japanese Encodings sun4-solaris-thread-multi::Encode::KR - Korean Encodings sun4-solaris-thread-multi::Encode::Symbol - Symbol Encodings sun4-solaris-thread-multi::Encode::TW - Taiwan-based Chinese Encodings sun4-solaris-thread-multi::Encode::Unicode - Various Unicode Transformation Formats sun4-solaris-thread-multi::IO::Pipe - supply object methods for pipes sun4-solaris-thread-multi::IO::File - supply object methods for filehandles sun4-solaris-thread-multi::IO::Select - OO interface to the select system call sun4-solaris-thread-multi::IO::Socket - Object interface to socket communications sun4-solaris-thread-multi::IO::Poll - Object interface to system poll call sun4-solaris-thread-multi::IO::Dir - supply object methods for directory handles sun4-solaris-thread-multi::IO::Handle - supply object methods for I/O handles sun4-solaris-thread-multi::IO::Seekable - supply seek based methods for I/O objects sun4-solaris-thread-multi::MIME::QuotedPrint - Encoding and decoding of quoted-printable strings sun4-solaris-thread-multi::MIME::Base64 - Encoding and decoding of base64 strings sun4-solaris-thread-multi::Sys::Hostname - Try every conceivable way to get hostname sun4-solaris-thread-multi::Sys::Syslog - Perl interface to the UNIX syslog(3) calls sun4-solaris-thread-multi::XS::APItest - Test the perl C API sun4-solaris-thread-multi::XS::Typemap - module to test the XS typemaps distributed with perl sun4-solaris-thread-multi::threads::shared - Perl extension for sharing data structures between threads Attribute::Handlers (0.78) - Simpler definition of attribute handlers Carp::Heavy - no user serviceable parts inside CGI::Apache - Backward compatibility module for CGI.pm CGI::Carp (1.27) - CGI routines for writing to the HTTPD (or other) error log CGI::Cookie (1.24) - Interface to Netscape Cookies CGI::Fast - CGI Interface for Fast CGI CGI::Pretty (1.08) - module to produce nicely formatted HTML code CGI::Push (1.04) - Simple Interface to Server Push CGI::Switch - Backward compatibility module for defunct CGI::Switch CGI::Util (1.4) - Internal utilities used by CGI module Class::ISA (0.32) - report the search path for a class's ISA tree Class::Struct (0.63) - declare struct-like datatypes as Perl classes Devel::SelfStubber (1.03) - generate stubs for a SelfLoading module Digest::base (1.00) - Digest base class Exporter::Heavy (5.57) - Exporter guts ExtUtils::Command (1.05) - utilities to replace common UNIX commands in Makefiles etc. ExtUtils::Constant (0.14) - generate XS code to import C header constants ExtUtils::Embed (1.250601) - Utilities for embedding Perl in C/C++ applications ExtUtils::Installed (0.08) - Inventory management of installed modules ExtUtils::Install (1.32) - install files from here to there ExtUtils::Liblist (1.01) - determine libraries to use and how to use them ExtUtils::MakeMaker (6.17) - Create a module Makefile ExtUtils::Manifest (1.42) - utilities to write and check a MANIFEST file ExtUtils::Mkbootstrap (1.15) - make a bootstrap file for use by DynaLoader ExtUtils::Mksymlists (1.19) - write linker options files for dynamic extension ExtUtils::MM_Any (0.07) - Platform-agnostic MM methods ExtUtils::MM_BeOS (1.04) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_Cygwin (1.06) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_DOS (0.02) - DOS specific subclass of ExtUtils::MM_Unix ExtUtils::MM_MacOS (1.07) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_NW5 (2.06) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM (0.04) - OS adjusted ExtUtils::MakeMaker subclass ExtUtils::MM_OS2 (1.04) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_Unix (1.42) - methods used by ExtUtils::MakeMaker ExtUtils::MM_UWIN (0.02) - U/WIN specific subclass of ExtUtils::MM_Unix ExtUtils::MM_VMS (5.70) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_Win32 (1.09) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_Win95 (0.03) - method to customize MakeMaker for Win9X ExtUtils::MY (0.01) - ExtUtils::MakeMaker subclass for customization ExtUtils::Packlist (0.04) - manage .packlist files ExtUtils::testlib (1.15) - add blib/* directories to @INC ExtUtils::Miniperl - write the C code for perlmain.c ExtUtils::Command::MM (0.03) - Commands for the MM's to use in Makefiles ExtUtils::MakeMaker::bytes (0.01) - Version agnostic bytes.pm ExtUtils::MakeMaker::vmsish (0.01) - Platform agnostic vmsish.pm File::Basename (2.72) - split a pathname into pieces File::CheckTree (4.3) - run many filetest checks on a tree File::Compare (1.1003) - Compare files or filehandles File::Copy (2.07) - Copy files or filehandles File::DosGlob (1.00) - DOS like globbing and then some File::Find (1.06) - Traverse a directory tree. File::Path (1.06) - create or remove directory trees File::Spec (0.87) - portably perform operations on file names File::stat (1.00) - by-name interface to Perl's built-in stat() functions File::Temp (0.14) - return name and handle of a temporary file safely File::Spec::Cygwin (1.1) - methods for Cygwin file specs File::Spec::Epoc (1.1) - methods for Epoc file specs File::Spec::Functions (1.3) - portably perform operations on file names File::Spec::Mac (1.4) - File::Spec for Mac OS (Classic) File::Spec::OS2 (1.2) - methods for OS/2 file specs File::Spec::Unix (1.5) - File::Spec for Unix, base for other File::Spec modules File::Spec::VMS - methods for VMS file specs File::Spec::Win32 (1.4) - methods for Win32 file specs Filter::Simple (0.78) - Simplified source filtering Getopt::Long (2.34) - Extended processing of command line options Getopt::Std (1.05) - Process single-character switches with switch clustering Hash::Util (0.05) - A selection of general-utility hash subroutines I18N::Collate (1.00) - compare 8-bit scalar data according to the current locale I18N::LangTags (0.29) - functions for dealing with RFC3066-style language tags I18N::LangTags::List (0.29) - tags and names for human languages IPC::Open2 (1.01) - open a process for both reading and writing IPC::Open3 (1.0105) - open a process for reading, writing, and error handling Math::BigFloat (1.42) - Arbitrary size floating point math package Math::BigInt (1.68) - Arbitrary size integer math package Math::BigRat (0.10) - arbitrarily big rationals Math::Complex (1.34) - complex numbers and associated mathematical functions Math::Trig (1.02) - trigonometric functions Math::BigInt::CalcEmu - Emulate low-level math with BigInt code Math::BigInt::Calc (0.38) - Pure Perl module to support Math::BigInt Memoize::AnyDBM_File (0.65) - glue to provide EXISTS for AnyDBM_File for Storable use Memoize::ExpireFile (1.01) - test for Memoize expiration semantics Memoize::Expire (1.00) - Plug-in module for automatic expiration of memoized values Memoize::ExpireTest (0.65) - test for Memoize expiration semantics Memoize::NDBM_File (0.65) - glue to provide EXISTS for NDBM_File for Storable use Memoize::SDBM_File (0.65) - glue to provide EXISTS for SDBM_File for Storable use Memoize::Storable (0.65) - store Memoized data in Storable database Net::Cmd (2.24) - Network Command class (as used by FTP, SMTP etc) Net::Config (1.10) - Local configuration data for libnet Net::Domain (2.19) - Attempt to evaluate the current host's internet name and domain Net::FTP (2.72) - FTP Client class Net::hostent (1.01) - by-name interface to Perl's built-in gethost*() functions Net::netent (1.00) - by-name interface to Perl's built-in getnet*() functions Net::Netrc (2.12) - OO interface to users netrc file Net::NNTP (2.22) - NNTP Client class Net::Ping (2.31) - check a remote host for reachability Net::POP3 (2.24) - Post Office Protocol 3 Client class (RFC1939) Net::protoent (1.00) - by-name interface to Perl's built-in getproto*() functions Net::servent (1.01) - by-name interface to Perl's built-in getserv*() functions Net::SMTP (2.26) - Simple Mail Transfer Protocol Client Net::Time (2.09) - time and daytime network client interface PerlIO::via::QuotedPrint (0.06) - PerlIO layer for quoted-printable strings Pod::Checker (1.41) - check pod documents for syntax errors Pod::Find (0.24) - find POD documents in directory trees Pod::Functions (1.02) - Group Perl's functions a la perlfunc.pod Pod::Html (1.0502) - module to convert pod files to HTML Pod::InputObjects (1.14) - objects representing POD input paragraphs, commands, etc. Pod::LaTeX (0.55) - Convert Pod data to formatted Latex Pod::Man (1.37) - Convert POD data to formatted *roff input Pod::ParseLink (1.06) - Parse an LEE formatting code in POD text Pod::Parser (1.14) - base class for creating POD filters and translators Pod::ParseUtils (0.3) - helpers for POD parsing and conversion Pod::Plainer (0.01) - Perl extension for converting Pod to old style Pod. Pod::PlainText (2.02) - Convert POD data to formatted ASCII text Pod::Select (1.13) - extract selected sections of POD from input Pod::Text (2.21) - Convert POD data to formatted ASCII text Pod::Usage (1.16) - print a usage message from embedded pod documentation Pod::Perldoc::ToChecker - let Perldoc check Pod for errors Pod::Perldoc::ToMan - let Perldoc render Pod as man pages Pod::Perldoc::ToNroff - let Perldoc convert Pod to nroff Pod::Perldoc::ToPod - let Perldoc render Pod as ... Pod! Pod::Perldoc::ToRtf - let Perldoc render Pod as RTF Pod::Perldoc::ToText - let Perldoc render Pod as plaintext Pod::Perldoc::ToTk - let Perldoc use Tk::Pod to render Pod Pod::Perldoc::ToXml - let Perldoc render Pod as XML Pod::Text::Color (1.04) - Convert POD data to formatted color ASCII text Pod::Text::Overstrike (1.1) - Convert POD data to formatted overstrike text Pod::Text::Termcap (1.11) - Convert POD data to ASCII text with format escapes Search::Dict (1.02) - search for key in dictionary file Term::ANSIColor (1.07) - Color screen output using ANSI escape sequences Term::Cap (1.08) - Perl termcap interface Term::Complete (1.401) - Perl word completion module Term::ReadLine (1.01) - Perl interface to various C packages. If no real package is found, substitutes stubs instead of basic functions. Test::Builder (0.17) - Backend for building test libraries Test::Harness (2.40) - Run Perl standard test scripts with statistics Test::More (0.47) - yet another framework for writing test scripts Test::Simple (0.47) - Basic utilities for writing tests. Test::Harness::Assert (0.02) - simple assert Test::Harness::Iterator (0.02) - Internal Test::Harness Iterator Test::Harness::Straps (0.19) - detailed analysis of test results Text::Abbrev (1.01) - create an abbreviation table from a list Text::Balanced (1.95) - Extract delimited text sequences from strings. Text::ParseWords (3.21) - parse text into an array of tokens or array of arrays Text::Soundex (1.01) - Implementation of the Soundex Algorithm as Described by Knuth Text::Tabs (98.112801) - expand and unexpand tabs per the unix expand(1) and unexpand(1) Text::Wrap (2001.09291) - line wrapping to form simple paragraphs Thread::Queue (2.00) - thread-safe queues Thread::Semaphore (2.01) - thread-safe semaphores Tie::Array (1.03) - base class for tied arrays Tie::File (0.97) - Access the lines of a disk file via a Perl array Tie::Handle (4.1) - base class definitions for tied handles Tie::Hash (1.01) - base class definitions for tied hashes Tie::Memoize (1.0) - add data to hash when needed Tie::RefHash (1.31) - use references as hash keys Tie::Scalar (1.00) - base class definitions for tied scalars Tie::SubstrHash (1.00) - Fixed-table-size, fixed-key-length hashing Time::gmtime (1.02) - by-name interface to Perl's built-in gmtime() function Time::Local (1.07) - efficiently compute time from local and GMT time Time::localtime (1.02) - by-name interface to Perl's built-in localtime() function Time::tm (1.00) - internal object used by Time::gmtime and Time::localtime Unicode::Collate (0.33) - Unicode Collation Algorithm Unicode::UCD (0.21) - Unicode character database User::grent (1.00) - by-name interface to Perl's built-in getgr*() functions User::pwent (1.00) - by-name interface to Perl's built-in getpw*() functions warnings::register (1.00) - warnings import function Encode::JP::H2Z (1.02) - internally used by Encode::JP::2022_JP* Encode::JP::JIS7 (1.12) - internally used by Encode::JP Encode::Unicode::UTF7 (0.02) - UTF-7 encoding Encode::KR::2022_KR (1.06) - internally used by Encode::KR Encode::MIME::Header (1.09) - MIME 'B' and 'Q' header encoding Encode::CN::HZ (1.05) - internally used by Encode::CN IO::Socket::INET (1.27) - Object interface for AF_INET domain sockets IO::Socket::UNIX (1.21) - Object interface for AF_UNIX domain sockets List::Util (1.13) - A selection of general-utility list subroutines Scalar::Util (1.13) - A selection of general-utility scalar subroutines GD (2.11) - Interface to Gd Graphics Library HTML::PullParser (2.07) - Alternative HTML::Parser interface HTML::Parser (3.35) - HTML parser class HTML::Entities (1.27) - Encode or decode strings with HTML entities HTML::TokeParser (2.28) - Alternative HTML::Parser interface HTML::LinkExtor (1.33) - Extract links from an HTML document HTML::Filter (2.10) - Filter HTML text through the parser HTML::HeadParser (2.18) - Parse section of a HTML document GD::Polyline (0.1) - Polyline object and Polygon utilities (including splines) for use with GD XML::Parser (2.34) - A perl module for parsing XML documents XML::Parser::Expat (2.34) - Lowlevel access to James Clark's expat XML parser XML::Parser::Style::Tree - XML::Parser::Style::Tree XML::Parser::Style::Subs - XML::Parser::Style::Subs XML::Parser::Style::Objects - XML::Parser::Style::Objects XML::Parser::Style::Debug - Debug style for XML::Parser XML::Parser::Style::Stream - Stream style for XML::Parser URI (1.30) - Uniform Resource Identifiers (absolute and relative) LWP (5.76) - The World-Wide Web library for Perl SVG (2.28) - Perl extension for generating Scalable Vector Graphics (SVG) documents Ace (1.87) - Object-Oriented Access to ACEDB Databases Heap (0.70) - Perl extensions for keeping data partially sorted Graph (0.20101) - graph operations sun4-solaris-thread-multi::GD - Interface to Gd Graphics Library sun4-solaris-thread-multi::HTML::PullParser - Alternative HTML::Parser interface sun4-solaris-thread-multi::HTML::Parser - HTML parser class sun4-solaris-thread-multi::HTML::Entities - Encode or decode strings with HTML entities sun4-solaris-thread-multi::HTML::TokeParser - Alternative HTML::Parser interface sun4-solaris-thread-multi::HTML::LinkExtor - Extract links from an HTML document sun4-solaris-thread-multi::HTML::Filter - Filter HTML text through the parser sun4-solaris-thread-multi::HTML::HeadParser - Parse section of a HTML document sun4-solaris-thread-multi::GD::Polyline - Polyline object and Polygon utilities (including splines) for use with GD sun4-solaris-thread-multi::XML::Parser - A perl module for parsing XML documents sun4-solaris-thread-multi::XML::Parser::Expat - Lowlevel access to James Clark's expat XML parser sun4-solaris-thread-multi::XML::Parser::Style::Tree - XML::Parser::Style::Tree sun4-solaris-thread-multi::XML::Parser::Style::Subs - XML::Parser::Style::Subs sun4-solaris-thread-multi::XML::Parser::Style::Objects - XML::Parser::Style::Objects sun4-solaris-thread-multi::XML::Parser::Style::Debug - Debug style for XML::Parser sun4-solaris-thread-multi::XML::Parser::Style::Stream - Stream style for XML::Parser URI::QueryParam - Additional query methods for URIs URI::WithBase (2.19) - URIs which remember their base URI::data - URI that contains immediate data URI::ldap (1.11) - LDAP Uniform Resource Locators URI::Heuristic (4.17) - Expand URI using heuristics URI::URL (5.03) - Uniform Resource Locators URI::file (4.14) - URI that maps to local file names URI::Split - Parse and compose URI strings URI::Escape (3.22) - Escape and unescape unsafe characters HTML::Tagset (3.03) - data tables useful in parsing HTML HTML::Form (1.038) - Class that represents an HTML form element LWP::RobotUA (1.23) - a class for well-behaved Web robots LWP::Protocol (1.41) - Base class for LWP protocols LWP::UserAgent (2.024) - Web user agent class LWP::MemberMixin - Member access mixin class LWP::Debug - debug routines for the libwww-perl library LWP::ConnCache (0.01) - Connection cache manager LWP::MediaTypes (1.30) - guess media type for a file or a URL LWP::DebugFile - routines for tracing/debugging LWP LWP::Simple (1.38) - simple procedural interface to LWP LWP::Authen::Ntlm - Library for enabling NTLM authentication (Microsoft) in LWP HTTP::Message (1.30) - HTTP style message base class HTTP::Status (1.28) - HTTP Status code processing HTTP::Daemon (1.33) - a simple http server class HTTP::Cookies (1.36) - HTTP cookie jars HTTP::Date (1.46) - date conversion routines HTTP::Request (1.34) - HTTP style request message HTTP::Negotiate (1.14) - choose a variant to serve HTTP::Response (1.41) - HTTP style response message HTTP::Headers (1.47) - Class encapsulating HTTP Message headers HTTP::Headers::Util (1.13) - Header value parsing utility functions HTTP::Request::Common (1.22) - Construct common HTTP::Request objects HTTP::Cookies::Netscape (1.26) - access to Netscape cookies files HTTP::Cookies::Microsoft - access to Microsoft cookies files Net::HTTP (1.00) - Low-level HTTP connection (client) Net::HTTP::NB (0.02) - Non-blocking HTTP client File::Listing (1.15) - parse directory listing WWW::RobotRules (1.26) - database of robots.txt-derived permissions WWW::RobotRules::AnyDBM_File (1.11) - Persistent RobotRules Bundle::LWP (1.10) - install all libwww-perl related modules SVG::DOM (1.01) - A library of DOM (Document Object Model) methods for SVG objects. SVG::Manual - Perl extension for generating Scalable Vector Graphics (SVG) documents SVG::XML (2.26) - Handle the XML generation bits for SVG.pm SVG::Element (2.26) - Generate the element bits for SVG.pm GD::SVG (0.25) - Seamlessly enable SVG output from scripts written using GD Ace::Iterator (1.51) - Iterate Across an ACEDB Query Ace::Local (1.05) - use giface, tace or gifaceclient to open a local connection to an Ace database Ace::Object (1.66) - Manipulate Ace Data Objects Ace::Model (1.51) - Get information about AceDB models Ace::Sequence (1.51) - Examine ACeDB Sequence Objects Ace::Graphics::GlyphFactory - Create Ace::Graphics::Glyphs Ace::Graphics::Glyph - Base class for Ace::Graphics::Glyph objects Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects Ace::Graphics::Fk - A dummy feature object used for generating panel key tracks Ace::Graphics::Panel - PNG graphics of Ace::Sequence::Feature objects Ace::Graphics::Glyph::box - The "box" glyph Ace::Graphics::Glyph::arrow - The "arrow" glyph Ace::Graphics::Glyph::toomany - The "too many to show" glyph ce::Graphics::Glyph::primers - The "STS primers" glyph Ace::Graphics::Glyph::ex - The "X" glyph Ace:::Sequence::Gene - Simple "Gene" Object Ace::Sequence::GappedAlignment (1.20) - Gapped alignment object Ace::Sequence::Multi - Combine Feature Tables from Multiple Databases Ace::Sequence::Feature - Examine Sequence Feature Tables Ace::Sequence::FeatureList - Lightweight Access to Features Ace::Sequence::Transcript - Simple "Gene" Object Ace::Sequence::Homol - Temporary Sequence Homology Class Ace::Browser::AceSubs - Subroutines for AceBrowser Ace::Browser::SiteDefs - Access to AceBrowser configuration files Ace::Browser::SearchSubs - Subroutines for AceBrowser search scripts IO::Lines (2.103) - IO:: interface for reading/writing an array of lines IO::Stringy (2.109) - I/O on in-core objects like strings and arrays IO::ScalarArray (2.103) - IO:: interface for reading/writing an array of scalars IO::Wrap (2.102) - wrap raw filehandles in IO::Handle interface IO::AtomicFile (2.101) - write a file which is updated atomically IO::Scalar (2.105) - IO:: interface for reading/writing a scalar IO::InnerFile (2.102) - define a file inside another file IO::WrapTie (2.102) - wrap tieable objects in IO::Handle interface IO::String (1.04) - Emulate file interface for in-core strings Mail::Cap (1.60) - Parse mailcap files Mail::Header (1.60) - manipulate mail RFC822 compliant headers Mail::Mailer (1.60) - Simple interface to electronic mailing mechanisms Mail::Send (1.60) - Simple electronic mail interface Mail::Filter (1.60) - Filter mail through multiple subroutines Mail::Field (1.60) - Base class for manipulation of mail header fields Mail::Internet (1.60) - manipulate Internet format (RFC 822) mail messages Mail::Util (1.60) - mail utility functions Mail::Address (1.60) - Parse mail addresses Mail::Field::AddrList (1.60) - object representation of e-mail address lists MIME::Body (5.403) - the body of a MIME message MIME::Entity (5.404) - class for parsed-and-decoded MIME message MIME::Head (5.403) - MIME message header (a subclass of Mail::Header) MIME::Words (5.404) - deal with RFC-1522 encoded words MIME::Tools (5.411) - modules for parsing (and creating!) MIME entities MIME::Decoder (5.403) - an object for decoding the body part of a MIME stream MIME::WordDecoder - decode RFC-1522 encoded words to a local representation MIME::Parser (5.406) - experimental class for parsing MIME streams MIME::Lite (3.01) - low-calorie MIME generator MIME::Decoder::Gzip64 (5.403) - decode a "base64" gzip stream MIME::Decoder::NBit (5.403) - encode/decode a "7bit" or "8bit" stream MIME::Decoder::Binary (5.403) - perform no encoding/decoding MIME::Decoder::UU (5.403) - decode a "uuencoded" stream MIME::Decoder::QuotedPrint (5.403) - encode/decode a "quoted-printable" stream MIME::Decoder::Base64 (5.403) - encode/decode a "base64" stream MIME::Field::ContDisp (5.403) - a "Content-disposition" field MIME::Field::ContType (5.403) - a "Content-type" field MIME::Field::ParamVal (5.403) - subclass of Mail::Field, for structured MIME fields MIME::Field::ConTraEnc (5.403) - a "Content-transfer-encoding" field MIME::Parser::Results - results of the last entity parsed MIME::Parser::Filer - manage file-output of the parser MIME::Parser::Reader - a line-oriented reader for a MIME::Parser SOAP::Test (0.55) - Test framework for SOAP::Lite SOAP::Lite (0.55) - Client and server side SOAP implementation SOAP::Transport::JABBER - Server/Client side JABBER support for SOAP::Lite SOAP::Transport::MAILTO (0.55) - Client side SMTP/sendmail support for SOAP::Lite SOAP::Transport::MQ - Server/Client side MQ support for SOAP::Lite SOAP::Transport::POP3 (0.55) - Server side POP3 support for SOAP::Lite SOAP::Transport::TCP (0.55) - Server/Client side TCP support for SOAP::Lite SOAP::Transport::IO (0.55) - Server side IO support for SOAP::Lite SOAP::Transport::HTTP (0.55) - Server/Client side HTTP support for SOAP::Lite SOAP::Transport::LOCAL (0.55) - Client side no-transport support for SOAP::Lite SOAP::Transport::FTP (0.55) - Client side FTP support for SOAP::Lite UDDI::Lite (0.55) - Library for UDDI clients in Perl XML::Twig (3.12) - A perl module for processing huge XML documents in tree mode. XML::Writer (0.4) - Perl extension for writing XML documents. XML::SAX2Perl - translate Java/CORBA style SAX methods to Perl methods XML::Perl2SAX (0.07) - translate Perl SAX methods to Java/CORBA style methods XML::ESISParser (0.07) - Perl SAX parser using nsgmls XML::Parser::Lite (0.55) - Lightweight regexp-based XML parser XML::Parser::PerlSAX (0.07) - Perl SAX parser using XML::Parser XML::Handler::Subs (0.07) - a PerlSAX handler base class for calling user-defined subs XML::Handler::Sample - a trivial PerlSAX handler XML::Handler::CanonXMLWriter (0.07) - output XML in canonical XML format XML::Handler::XMLWriter (0.07) - a PerlSAX handler for writing readable XML XML::PatAct::MatchName (0.07) - A pattern module for matching element names XML::PatAct::ActionTempl - An action module for XML::PatAct::ToObjects (0.07) - An action module for creating Perl objects XML::PatAct::PatternTempl - A pattern module for XML::PatAct::Amsterdam (0.07) - An action module for simplistic style-sheets XMLRPC::Lite (0.55) - client and server implementation of XML-RPC protocol XMLRPC::Test (0.55) - Test framework for XMLRPC::Lite XMLRPC::Transport::POP3 (0.55) - Server side POP3 support for XMLRPC::Lite XMLRPC::Transport::TCP (0.55) - Server/Client side TCP support for XMLRPC::Lite XMLRPC::Transport::HTTP (0.55) - Server/Client side HTTP support for XMLRPC::Lite Apache::SOAP - mod_perl-based SOAP server with minimum configuration Apache::XMLRPC::Lite - mod_perl-based XML-RPC server with minimum configuration Text::Shellwords (1.03) - Text::Shellwords Heap::Binary (0.70) - a Perl extension for keeping data partially sorted Heap::Binomial (0.70) - a Perl extension for keeping data partially sorted Heap::Elem (0.70) - Perl extension for elements to be put in Heaps Heap::Fibonacci (0.70) - a Perl extension for keeping data partially sorted Heap::Elem::Num (0.70) - Perl extension for Numeric Heap Elements Heap::Elem::NumRev (0.70) - Perl extension for Reversed Numeric Heap Elements Heap::Elem::Ref (0.70) - Perl extension for Object Reference Heap Elements Heap::Elem::RefRev (0.70) - Perl extension for reversed Object Reverence Heap Elements Heap::Elem::Str (0.70) - Perl extension for String Heap Elements Heap::Elem::StrRev (0.70) - Perl extension for Reversed String Heap Elements Graph::Directed - directed graphs Graph::Base - graph base class Graph::Undirected - directed graphs Graph::BFS - graph breadth-first search Graph::HeapElem (0.01) - internal use only Graph::DFS - graph depth-first search Graph::Traversal - graph traversal Data::Grove (0.07) - support for deeply nested structures Data::Grove::Parent (0.07) - provide parent properties to Data::Grove objects Data::Grove::Visitor (0.07) - add visitor/callback methods to Data::Grove objects Bio::WebAgent (1.4) - A base class for Web (any protocol) access Bio::TreeIO (1.4) - Parser for Tree files Bio::LocationI (1.4) - Abstract interface of a Location on a Sequence Bio::Taxonomy (1.4) - representing Taxonomy. Bio::DBLinkContainerI (1.4) - Abstract interface for any object wanting to use database cross references Bio::SeqIO (1.4) - Handler for SeqIO Formats Bio::AnalysisI (1.4) - An interface to any (local or remote) analysis tool Bio::MapIO (1.4) - A Map Factory object Bio::SimpleAnalysisI (1.4) - A simple interface to any (local or remote) analysis tool Bio::IdCollectionI (1.4) - interface for objects with multiple identifiers Bio::UpdateableSeqI (1.4) - Descendant of Bio::SeqI that allows updates Bio::Biblio (1.4) - A Bibliographic Query Service module Bio::AlignIO (1.4) - Handler for AlignIO Formats Bio::Seq (1.4) - Sequence object, with features Bio::DescribableI (1.4) - interface for objects with human readable names and descriptions Bio::RangeI (1.4) - Range interface Bio::OntologyIO (1.4) - Parser factory for Ontology formats Bio::FeatureHolderI (1.4) - the base interface an object with features must implement Bio::AnalysisResultI (1.4) - Interface for analysis result objects Bio::SeqAnalysisParserI (1.4) - Sequence analysis output parser interface Bio::SeqI (1.4) - Abstract Interface of Sequence (with features) Bio::AnalysisParserI (1.4) - Generic analysis output parser interface Bio::SearchIO (1.4) - Driver for parsing Sequence Database Searches (Blast,FASTA,...) Bio::SearchDist (Can't locate Bio/Ext/Align.pm in @INC (@INC contains: /usr/lib/perl5/5.8.3/sun4-solaris-thread-multi /usr/lib/perl5/5.8.3 /usr/lib/perl5/site_perl/5.8.3/sun4-solaris-thread-multi /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl .) at /usr/lib/perl5/site_perl/5.8.3/Bio/SearchDist.pm line 109.) - A perl wrapper around Sean Eddy's histogram object Bio::AnnotationCollectionI (1.4) - Interface for annotation collections Bio::SeqFeatureI (1.4) - Abstract interface of a Sequence Feature Bio::PrimarySeq (1.4) - Bioperl lightweight Sequence Object Bio::AnnotationI (1.4) - Annotation interface Bio::Graphics (1.4) - Generate GD images of Bio::Seq objects Bio::PrimarySeqI (1.4) - Interface definition for a Bio::PrimarySeq Bio::SimpleAlign (1.4) - Multiple alignments held as a set of sequences Bio::ClusterIO (1.4) - Handler for Cluster Formats Bio::IdentifiableI (1.4) - interface for objects with identifiers Bio::Species (1.4) - Generic species object Bio::ClusterI (1.4) - Cluster Interface Bio::LocatableSeq (1.4) - A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. Bio::DasI (1.4) - DAS-style access to a feature database Bio::SeqUtils (1.4) - Additional methods for PrimarySeq objects Bio::Range (1.4) - Pure perl RangeI implementation Bio::Perl (1.4) - Functional access to BioPerl for people who don't know objects Bio::AnnotatableI (1.4) - the base interface an annotatable object must implement Bio::PopGen::MarkerI (1.4) - A Population Genetic conceptual marker Bio::PopGen::PopulationI (1.4) - Interface for Populations Bio::PopGen::Genotype (1.4) - An implementation of a genotype which is an allele container Bio::PopGen::IO (1.4) - Input individual,marker,allele information Bio::PopGen::Population (1.4) - A population of individuals Bio::PopGen::IndividualI (1.4) - An individual who has Genotype or Sequence Results Bio::PopGen::PopStats (1.4) - A collection of methods for calculating statistics about a population or sets of populations Bio::PopGen::GenotypeI (1.4) - A marker and alleles for a specific individual Bio::PopGen::Statistics (1.4) - Population Genetics statistical tests Bio::PopGen::Individual (1.4) - An implementation of an Individual who has Genotype or Sequence Results Bio::PopGen::Marker (1.4) - A genetic marker which one uses to generate genotypes Bio::PopGen::Simulation::Coalescent (1.4) - A Coalescent simulation factory Bio::PopGen::Simulation::GeneticDrift (1.4) - A simple genetic drift simulation Bio::PopGen::IO::prettybase (1.4) - Extract individual allele data from PrettyBase format Bio::PopGen::IO::csv (1.4) - Bio::PopGen::IO::csv -Extract individual allele data from a CSV parser Bio::Matrix::MatrixI (1.4) - An interface for describing a Matrix Bio::Matrix::Generic (1.4) - A generic matrix implementation Bio::Matrix::Scoring (1.4) - Object which can hold scoring matrix information Bio::Matrix::IO (1.4) - A factory for Matrix parsing Bio::Matrix::PhylipDist (1.4) - A Phylip Distance Matrix object Bio::Matrix::PSM::Psm (1.4) - handle combination of site matricies Bio::Matrix::PSM::PsmI (1.4) - abstract interface to handler of site matricies Bio::Matrix::PSM::InstanceSite (1.4) - A PSM site occurance Bio::Matrix::PSM::IO (1.4) - Bio::Matrix::PSM::InstanceSiteI (1.4) - Bio::Matrix::PSM::PsmHeader (1.4) - PSM mast parser implementation Bio::Matrix::PSM::SiteMatrix (1.4) - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) Bio::Matrix::PSM::SiteMatrixI (1.4) - SiteMatrix interface, holds a position scoring matrix (or position weight matrix) Bio::Matrix::PSM::PsmHeaderI (1.4) - Bio::Matrix::PSM::IO::transfac (1.4) - PSM transfac parser Bio::Matrix::PSM::IO::mast (1.4) - PSM mast parser implementation Bio::Matrix::PSM::IO::meme (1.4) - PSM meme parser implementation Bio::Matrix::IO::phylip (1.4) - A parser for PHYLIP distance matricies Bio::Matrix::IO::scoring (1.4) - A parser for PAM/BLOSUM matricies Bio::Tools::GuessSeqFormat (1.4) - Module for determining the sequence format of the contents of a file, a string, or through a filehandle. Bio::Tools::RepeatMasker (1.4) - DESCRIPTION of Object Bio::Tools::Gel (1.4) - Calculates relative electrophoretic migration distances Bio::Tools::SeqPattern (1.4) - Bioperl object for a sequence pattern or motif Bio::Tools::Prints (1.4) - Parser for FingerPRINTScanII program Bio::Tools::dpAlign - Perl extension to do pairwise dynamic programming sequence alignment Bio::Tools::pICalculator (1.4) - pICalculator Bio::Tools::SeqStats (1.4) - Object holding statistics for one particular sequence Bio::Tools::QRNA (1.4) - A Parser for qrna output Bio::Tools::Sigcleave (1.4) - Bioperl object for sigcleave analysis Bio::Tools::ESTScan (1.4) - Results of one ESTScan run Bio::Tools::AnalysisResult (1.4) - Base class for analysis result objects and parsers Bio::Tools::ECnumber (1.4) - representation of EC numbers Bio::Tools::Pseudowise (1.4) - Results of one Pseudowise run Bio::Tools::Genscan (1.4) - Results of one Genscan run Bio::Tools::Blast (1.4) - Bioperl BLAST sequence analysis object Bio::Tools::GFF (1.4) - A Bio::SeqAnalysisParserI compliant GFF format parser Bio::Tools::RandomDistFunctions (1.4) - A set of routines useful for generating random data in different distributions Bio::Tools::Primer3 (1.4) - Create input for and work with the output from the program primer3 Bio::Tools::Seg (1.4) - parse Seg output (filter low complexity protein sequence) Bio::Tools::Signalp (1.4) - Bio::Tools::Signalp Bio::Tools::BPbl2seq (1.4) - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm. Bio::Tools::WWW (1.4) - Bioperl manager for web resources related to biology. Bio::Tools::IUPAC (1.4) - Generates unique Seq objects from an ambiguous Seq object Bio::Tools::SiRNA (1.4) - Perl object for designing small inhibitory RNAs. Bio::Tools::Promoterwise (1.4) - DESCRIPTION of Object Bio::Tools::Geneid (1.4) - Results of one geneid run Bio::Tools::Hmmpfam (1.4) - Bio::Tools::Hmmpfam Bio::Tools::Grail (1.4) - Results of one Grail run Bio::Tools::CodonTable (1.4) - Bioperl codon table object Bio::Tools::AlignFactory - Base object for alignment factories Bio::Tools::MZEF (1.4) - Results of one MZEF run Bio::Tools::Est2Genome (1.4) - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects Bio::Tools::PrositeScan (1.4) - Parser for ps_scan result Bio::Tools::FootPrinter (1.4) - DESCRIPTION of Object Bio::Tools::Coil (1.4) - Bio::Tools::Coil Bio::Tools::Lucy (1.4) - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR Bio::Tools::OddCodes (1.4) - Object holding alternative alphabet coding for one protein sequence Bio::Tools::SeqAnal (1.4) - Bioperl sequence analysis base class. Bio::Tools::Genemark (1.4) - Results of one Genemark run Bio::Tools::BPpsilite (1.4) - Lightweight BLAST parser for (iterated) psiblast reports Bio::Tools::Profile (1.4) - parse Profile output Bio::Tools::Glimmer (1.4) - A parser for GLIMMER gene predictions Bio::Tools::RestrictionEnzyme (1.4) - Bioperl object for a restriction endonuclease (cuts DNA at specific locations) Bio::Tools::BPlite (1.4) - Lightweight BLAST parser Bio::Tools::Genewise (1.4) - Results of one Genewise run Bio::Tools::Genomewise (1.4) - Results of one Genomewise run Bio::Tools::Eponine (1.4) - Results of one Eponine run Bio::Tools::Tmhmm (1.4) - parse TmHMM output (transmembrane HMM) Bio::Tools::Blat (1.4) - Bio::Tools::Blat Bio::Tools::EPCR (1.4) - Parse ePCR output and make features Bio::Tools::pSW - pairwise Smith Waterman object Bio::Tools::SeqWords (1.4) - Object holding n-mer statistics for one sequence Bio::Tools::Blast::Sbjct (1.4) - Bioperl BLAST "Hit" object Bio::Tools::Blast::HTML (1.4) - Bioperl Utility module for HTML formatting Blast reports Bio::Tools::Blast::HSP (1.4) - Bioperl BLAST High-Scoring Segment Pair object Bio::Tools::HMMER::Set (1.4) - Set of identical domains from HMMER matches Bio::Tools::HMMER::Results (1.4) - Object representing HMMER output results Bio::Tools::HMMER::Domain (1.4) - One particular domain hit from HMMER Bio::Tools::Run::RemoteBlast (1.4) - Object for remote execution of the NCBI Blast via HTTP Bio::Tools::Run::StandAloneBlast (1.4) - Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast. Bio::Tools::Run::WrapperBase (1.4) - A Base object for wrappers around executables Bio::Tools::Analysis::SimpleAnalysisBase (1.4) - abstact superclass for SimpleAnalysis implementations Bio::Tools::Analysis::Protein::ELM (1.4) - =head1 SYNOPSIS Bio::Tools::Analysis::Protein::GOR4 (1.4) - a wrapper around GOR4 protein secondary structure prediction server Bio::Tools::Analysis::Protein::HNN (1.4) - a wrapper around HNN protein secondary structure prediction server Bio::Tools::Analysis::Protein::Sopma (1.4) - a wrapper around Sopma protein secondary structure prediction server Bio::Tools::Analysis::Protein::NetPhos (1.4) - a wrapper around NetPhos server Bio::Tools::Analysis::Protein::Scansite (1.4) - a wrapper around the Scansite server Bio::Tools::Analysis::Protein::Domcut (1.4) - a wrapper around Domcut server Bio::Tools::Analysis::Protein::Mitoprot (1.4) - a wrapper around Mitoprot server Bio::Tools::Analysis::DNA::ESEfinder (1.4) - a wrapper around ESEfinder server Bio::Tools::Phylo::PAML (1.4) - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 Bio::Tools::Phylo::Molphy (1.4) - DESCRIPTION of Object Bio::Tools::Phylo::PAML::ModelResult (1.4) - A container for NSSite Model Result from PAML Bio::Tools::Phylo::PAML::Result (1.4) - A PAML result set object Bio::Tools::Phylo::Molphy::Result (1.4) - DESCRIPTION of Object Bio::Tools::Phylo::Phylip::ProtDist (1.4) - DESCRIPTION of Object Bio::Tools::Sim4::Exon (1.4) - A single exon determined by an alignment Bio::Tools::Sim4::Results (1.4) - Results of one Sim4 run Bio::Tools::Primer::AssessorI - interface for assessing primer pairs Bio::Tools::Primer::Feature - position of a single primer Bio::Tools::Primer::Pair - two primers on left and right side Bio::Tools::Primer::Assessor::Base - base class for common assessor things Bio::Tools::Alignment::Trim (1.4) - A kludge to do specialized trimming of sequence based on quality. Bio::Tools::Alignment::Consed (1.4) - A module to work with objects from consed .ace files Bio::Tools::BPlite::Sbjct (1.4) - A Blast Subject (database search Hit) Bio::Tools::BPlite::HSP (1.4) - Blast report High Scoring Pair (HSP) Bio::Tools::BPlite::Iteration (1.4) - object for parsing single iteration of a PSIBLAST report Bio::Tools::Prediction::Gene (1.4) - a predicted gene structure feature Bio::Tools::Prediction::Exon (1.4) - A predicted exon feature Bio::Tools::EMBOSS::Palindrome (1.4) - parse EMBOSS palindrome output Bio::LiveSeq::ChainI (1.4) - Double linked chain data structure Bio::LiveSeq::Mutation (1.4) - Mutation event descriptor class Bio::LiveSeq::AARange (1.4) - AARange abstract class for LiveSeq Bio::LiveSeq::SeqI (1.4) - Abstract sequence interface class for LiveSeq Bio::LiveSeq::Repeat_Unit (1.4) - Repeat_Unit class for LiveSeq Bio::LiveSeq::DNA (1.4) - DNA object for LiveSeq Bio::LiveSeq::Transcript (1.4) - Transcript class for LiveSeq Bio::LiveSeq::Range (1.4) - Range abstract class for LiveSeq Bio::LiveSeq::Repeat_Region (1.4) - Repeat_Region class for LiveSeq Bio::LiveSeq::Intron (1.4) - Range abstract class for LiveSeq Bio::LiveSeq::Gene (1.4) - Range abstract class for LiveSeq Bio::LiveSeq::Translation (1.4) - Translation class for LiveSeq Bio::LiveSeq::Prim_Transcript (1.4) - Prim_Transcript class for LiveSeq Bio::LiveSeq::Exon (1.4) - Range abstract class for LiveSeq Bio::LiveSeq::Chain (1.4) - DoubleChain DataStructure for Perl Bio::LiveSeq::Mutator (1.4) - Package mutating LiveSequences Bio::LiveSeq::IO::Loader (1.4) - Parent Loader for LiveSeq Bio::LiveSeq::IO::SRS - Loader for LiveSeq from EMBL entries with SRS Bio::LiveSeq::IO::BioPerl (1.4) - Loader for LiveSeq from EMBL entries with BioPerl Bio::AlignIO::mega (1.4) - Parse and Create MEGA format data files Bio::AlignIO::prodom (1.4) - prodom sequence input/output stream Bio::AlignIO::emboss (1.4) - Parse EMBOSS alignment output (from applications water and needle) Bio::AlignIO::mase (1.4) - mase sequence input/output stream Bio::AlignIO::phylip (1.4) - PHYLIP format sequence input/output stream Bio::AlignIO::maf (1.4) - Multipla Alignment Format sequence input stream Bio::AlignIO::pfam (1.4) - pfam sequence input/output stream Bio::AlignIO::nexus (1.4) - NEXUS format sequence input/output stream Bio::AlignIO::bl2seq (1.4) - bl2seq sequence input/output stream Bio::AlignIO::msf (1.4) - msf sequence input/output stream Bio::AlignIO::psi (1.4) - Read/Write PSI-BLAST profile alignment files Bio::AlignIO::clustalw (1.4) - clustalw sequence input/output stream Bio::AlignIO::fasta (1.4) - FastA MSA Sequence input/output stream Bio::AlignIO::metafasta (1.4) - Metafasta MSA Sequence input/output stream Bio::AlignIO::stockholm (1.4) - stockholm sequence input/output stream Bio::AlignIO::meme (1.4) - meme sequence input/output stream Bio::AlignIO::selex (1.4) - selex sequence input/output stream Bio::Factory::ObjectFactory (1.4) - Instantiates a new Bio::Root::RootI (or derived class) through a factory Bio::Factory::SeqAnalysisParserFactoryI (1.4) - interface describing objects capable of creating SeqAnalysisParserI compliant parsers Bio::Factory::LocationFactoryI (1.4) - DESCRIPTION of Interface Bio::Factory::DriverFactory (1.4) - Base class for factory classes loading drivers Bio::Factory::ObjectFactoryI (1.4) - A General object creator factory Bio::Factory::HitFactoryI (1.4) - Interface for an object that builds Bio::Search::Hit::HitI objects Bio::Factory::ApplicationFactoryI (1.4) - Interface class for Application Factories Bio::Factory::FTLocationFactory (1.4) - A FeatureTable Location Parser Bio::Factory::SequenceProcessorI (1.4) - Interface for chained sequence processing algorithms Bio::Factory::MapFactoryI (1.4) - A Factory for getting markers Bio::Factory::AnalysisI (1.4) - An interface to analysis tool factory Bio::Factory::ObjectBuilderI (1.4) - Interface for an object builder Bio::Factory::ResultFactoryI (1.4) - Interface for an object that builds Bio::Search::Result::ResultI objects Bio::Factory::SequenceFactoryI (1.4) - This interface allows for generic building of sequences in factories which create sequences (like SeqIO) Bio::Factory::SequenceStreamI (1.4) - Interface describing the basics of a Sequence Stream. Bio::Factory::SeqAnalysisParserFactory (1.4) - class capable of creating SeqAnalysisParserI compliant parsers Bio::Factory::TreeFactoryI (1.4) - Factory Interface for getting and writing trees from/to a data stream Bio::SearchIO::megablast (1.4) - a driver module for Bio::SearchIO to parse megablast reports (format 0) Bio::SearchIO::fasta (1.4) - A SearchIO parser for FASTA results Bio::SearchIO::blasttable (1.4) - Driver module for SearchIO for parsing NCBI -m 8/9 format Bio::SearchIO::wise (1.4) - Parsing of wise output as alignments Bio::SearchIO::hmmer (1.4) - A parser for HMMER output (hmmpfam, hmmsearch) Bio::SearchIO::psl (1.4) - A parser for PSL output (UCSC) Bio::SearchIO::axt (1.4) - a parser for axt format reports Bio::SearchIO::sim4 (1.4) - parser for Sim4 alignments Bio::SearchIO::waba (1.4) - SearchIO parser for Jim Kent WABA program alignment output Bio::SearchIO::exonerate (1.4) - parser for Exonerate Bio::SearchIO::SearchResultEventBuilder (1.4) - Event Handler for SearchIO events. Bio::SearchIO::blast (1.4) - Event generator for event based parsing of blast reports Bio::SearchIO::FastHitEventBuilder (1.4) - Event Handler for SearchIO events. Bio::SearchIO::EventHandlerI (1.4) - An abstract Event Handler for Search Result parsing Bio::SearchIO::SearchWriterI (1.4) - Interface for outputting parsed Search results Bio::SearchIO::IteratedSearchResultEventBuilder (1.4) - Event Handler for SearchIO events. Bio::SearchIO::blastxml (1.4) - A SearchIO implementation of NCBI Blast XML parsing. Bio::SearchIO::Writer::HSPTableWriter (1.4) - Tab-delimited data for Bio::Search::HSP::HSPI objects Bio::SearchIO::Writer::GbrowseGFF (1.4) - Interface for outputting parsed search results in Gbrowse GFF format Bio::SearchIO::Writer::BSMLResultWriter (1.4) - DESCRIPTION of Object Bio::SearchIO::Writer::ResultTableWriter (1.4) - Outputs tab-delimited data for each Bio::Search::Result::ResultI object. Bio::SearchIO::Writer::HitTableWriter (1.4) - Tab-delimited data for Bio::Search::Hit::HitI objects Bio::SearchIO::Writer::TextResultWriter (1.4) - Object to implement writing a Bio::Search::ResultI in Text. Bio::SearchIO::Writer::HTMLResultWriter (1.4) - Object to implement writing a Bio::Search::ResultI in HTML. Bio::DB::Flat (1.4) - Interface for indexed flat files Bio::DB::SwissProt (1.4) - Database object interface to SwissProt retrieval Bio::DB::BiblioI (1.4) - An interface to a Bibliographic Query Service Bio::DB::Failover (1.4) - A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs Bio::DB::UpdateableSeqI (1.4) - An interface for writing to a database of sequences. Bio::DB::RefSeq (1.4) - Database object interface for RefSeq retrieval Bio::DB::NCBIHelper (1.4) - A collection of routines useful for queries to NCBI databases. Bio::DB::Fasta (1.4) - Fast indexed access to a directory of fasta files Bio::DB::RandomAccessI (1.4) - Abstract interface for a sequence database Bio::DB::BioFetch (1.4) - Database object interface to BioFetch retrieval Bio::DB::WebDBSeqI (1.4) - Object Interface to generalize Web Databases for retrieving sequences Bio::DB::SeqI (1.4) - Abstract Interface for Sequence databases Bio::DB::GenBank (1.4) - Database object interface to GenBank Bio::DB::MeSH (1.4) - Term retrieval from a Web MeSH database Bio::DB::EMBL (1.4) - Database object interface for EMBL entry retrieval Bio::DB::DBFetch (1.4) - Database object for retrieving using the dbfetch script Bio::DB::Taxonomy (1.4) - Access to a taxonomy database Bio::DB::Ace (1.4) - Database object interface to ACeDB servers Bio::DB::QueryI (1.4) - Object Interface to queryable sequence databases Bio::DB::InMemoryCache (1.4) - Abstract interface for a sequence database Bio::DB::FileCache (1.4) - In file cache for BioSeq objects Bio::DB::XEMBL - Database object interface for XEMBL entry retrieval Bio::DB::XEMBLService (1.4) - SOAP service definition for XEMBL Bio::DB::CUTG (1.4) - for access to the Codon usage Database at http://www.kazusa.or.jp/codon. Bio::DB::Universal (1.4) - Artificial database that delegates to specific databases Bio::DB::GFF (1.4) - Storage and retrieval of sequence annotation data Bio::DB::GDB (1.4) - Database object interface to GDB HTTP query Bio::DB::Registry (1.4) - Access to the Open Bio Database Access registry scheme Bio::DB::GenPept (1.4) - Database object interface to GenPept Bio::DB::GFF::Feature (1.4) - A relative segment identified by a feature type Bio::DB::GFF::Typename (1.4) - The name of a feature type Bio::DB::GFF::Homol (1.4) - A segment of DNA that is homologous to another Bio::DB::GFF::Segment (1.4) - Simple DNA segment object Bio::DB::GFF::Featname (1.4) - The name of a feature Bio::DB::GFF::Aggregator (1.4) - Aggregate GFF groups into composite features Bio::DB::GFF::RelSegment (1.4) - Sequence segment with relative coordinate support Bio::DB::GFF::Aggregator::ucsc_unigene (1.4) - UCSC UniGene aggregator Bio::DB::GFF::Aggregator::ucsc_acembly (1.4) - UCSC acembly aggregator Bio::DB::GFF::Aggregator::ucsc_sanger22 (1.4) - UCSC sanger22 aggregator Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo (1.4) - UCSC sanger22pseudo aggregator Bio::DB::GFF::Aggregator::alignment (1.4) - Alignment aggregator Bio::DB::GFF::Aggregator::match (1.4) - Match aggregator Bio::DB::GFF::Aggregator::ucsc_softberry (1.4) - UCSC softberry aggregator Bio::DB::GFF::Aggregator::ucsc_twinscan (1.4) - UCSC twinscan aggregator Bio::DB::GFF::Aggregator::transcript (1.4) - Transcript aggregator Bio::DB::GFF::Aggregator::none (1.4) - No aggregation Bio::DB::GFF::Aggregator::ucsc_refgene (1.4) - UCSC refGene aggregator Bio::DB::GFF::Aggregator::clone (1.4) - Clone aggregator Bio::DB::GFF::Aggregator::coding (1.4) - The Coding Region Aggregator Bio::DB::GFF::Aggregator::ucsc_genscan (1.4) - UCSC genscan aggregator Bio::DB::GFF::Aggregator::processed_transcript (1.4) - Sequence Ontology Transcript Bio::DB::GFF::Aggregator::ucsc_ensgene (1.4) - UCSC ensGene aggregator Bio::DB::GFF::Adaptor::memory (1.4) - Database adaptor for a specific mysql schema Bio::DB::GFF::Adaptor::memory_iterator (1.4) - iterator for Bio::DB::GFF::Adaptor::memory Bio::DB::GFF::Adaptor::dbi - Database adaptor for DBI (SQL) databases Bio::DB::GFF::Adaptor::biofetch_oracle - Cache BioFetch objects in a Bio::DB::GFF database Bio::DB::GFF::Adaptor::biofetch - Cache BioFetch objects in a Bio::DB::GFF database Bio::DB::GFF::Adaptor::ace (1.4) - ace interface (for multiple inheritance) Bio::DB::GFF::Adaptor::dbi::caching_handle - Cache for database handles Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema Bio::DB::GFF::Adaptor::dbi::mysql - Database adaptor for a specific mysql schema Bio::DB::GFF::Adaptor::dbi::mysqlopt - Deprecated database adaptor Bio::DB::GFF::Adaptor::dbi::mysqlace - Unholy union between mysql GFF database and acedb database Bio::DB::GFF::Adaptor::dbi::iterator (1.4) - iterator for Bio::DB::GFF::Adaptor::dbi Bio::DB::GFF::Adaptor::dbi::oracleace - Unholy union between oracle GFF database and acedb database Bio::DB::GFF::Adaptor::dbi::oracle - Database adaptor for a specific oracle schema Bio::DB::GFF::Util::Rearrange (1.4) - rearrange utility Bio::DB::GFF::Util::Binning (1.4) - binning utility for Bio::DB::GFF index Bio::DB::Biblio::biofetch (1.4) - A BioFetch-based access to a bibliographic citation retrieval Bio::DB::Biblio::soap (1.4) - A SOAP-based access to a bibliographic query service Bio::DB::Query::WebQuery (1.4) - Helper class for web-based sequence queryies Bio::DB::Query::GenBank (1.4) - Build a GenBank Entrez Query Bio::DB::Flat::BDB (1.4) - Interface for BioHackathon standard BDB-indexed flat file Bio::DB::Flat::BinarySearch (1.4) - BinarySearch search indexing system for sequence files Bio::DB::Flat::BDB::swiss (1.4) - swissprot adaptor for Open-bio standard BDB-indexed flat file Bio::DB::Flat::BDB::genbank (1.4) - genbank adaptor for Open-bio standard BDB-indexed flat file Bio::DB::Flat::BDB::fasta (1.4) - fasta adaptor for Open-bio standard BDB-indexed flat file Bio::DB::Flat::BDB::swissprot (1.4) - swissprot adaptor for Open-bio standard BDB-indexed flat file Bio::DB::Flat::BDB::embl (1.4) - embl adaptor for Open-bio standard BDB-indexed flat file Bio::DB::Taxonomy::entrez (1.4) - Taxonomy Entrez driver Bio::DB::Taxonomy::flatfile (1.4) - An implementation of Bio::DB::Taxonomy which uses local flat files Bio::Search::Processor (1.4) - DESCRIPTION of Object Bio::Search::BlastUtils (1.4) - Utility functions for Bio::Search:: BLAST objects Bio::Search::GenericDatabase (1.4) - Generic implementation of Bio::Search::DatabaseI Bio::Search::SearchUtils (1.4) - Utility functions for Bio::Search:: objects Bio::Search::DatabaseI (1.4) - Interface for a database used in a sequence search Bio::Search::HSP::PSLHSP (1.4) - A HSP for PSL output Bio::Search::HSP::WABAHSP (1.4) - HSP object suitable for describing WABA alignments Bio::Search::HSP::PsiBlastHSP (1.4) - Bioperl BLAST High-Scoring Pair object Bio::Search::HSP::FastaHSP (1.4) - HSP object for FASTA spcific data Bio::Search::HSP::GenericHSP (1.4) - A "Generic" implementation of a High Scoring Pair B Bio::Search::Hit::HitI objects Bio::Search::Hit::HitI (1.4) - Interface for a hit in a similarity search result Bio::Search::Hit::BlastHit (1.4) - Blast-specific subclass of Bio::Search::Hit::GenericHit Bio::Search::Hit::HMMERHit (1.4) - A Hit module for HMMER hits Bio::Search::Hit::GenericHit (1.4) - A generic implementation of the Bio::Search::Hit::HitI interface Bio::Search::Hit::Fasta (1.4) - Hit object specific for Fasta-generated hits Bio::Search::Result::HMMERResult (1.4) - A Result object for HMMER results Bio::Search::Result::ResultI (1.4) - Abstract interface to Search Result objects Bio::Search::Result::BlastResult (1.4) - Blast-specific subclass of Bio::Search::Result::GenericResult Bio::Search::Result::WABAResult (1.4) - Result object for WABA alignment output Bio::Search::Result::ResultFactory (1.4) - A factory to create Bio::Search::Result::ResultI objects Bio::Search::Result::GenericResult (1.4) - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. Bio::Search::Iteration::GenericIteration (1.4) - A generic implementation of the Bio::Search::Iteration::IterationI interface. Bio::Search::Iteration::IterationI (1.4) - Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. Bio::Cluster::UniGeneI (1.4) - abstract interface of UniGene object Bio::Cluster::UniGene (1.4) - UniGene object Bio::Cluster::FamilyI (1.4) - Family Interface Bio::Cluster::ClusterFactory (1.4) - Instantiates a new Bio::ClusterI (or derived class) through a factory Bio::Cluster::SequenceFamily (1.4) - Sequence Family object Bio::Biblio::PubmedBookArticle (1.4) - Representation of a PUBMED book article Bio::Biblio::Provider (1.4) - Representation of a general provider Bio::Biblio::BiblioBase (1.4) - An abstract base for other biblio classes Bio::Biblio::IO (1.4) - Handling the bibliographic references Bio::Biblio::Thesis (1.4) - Representation of thesis Bio::Biblio::Article (1.4) - Representation of a general article Bio::Biblio::Organisation (1.4) - Representation of an organisation Bio::Biblio::MedlineJournalArticle (1.4) - Representation of a MEDLINE journal article Bio::Biblio::BookArticle (1.4) - Representation of a book article Bio::Biblio::Journal (1.4) - Representation of a journal Bio::Biblio::PubmedJournalArticle (1.4) - Representation of a PUBMED journal article Bio::Biblio::Ref (1.4) - Representation of a bibliographic reference Bio::Biblio::TechReport (1.4) - Representation of a technical report Bio::Biblio::Person (1.4) - Representation of a person Bio::Biblio::WebResource (1.4) - Representation of a web resource Bio::Biblio::MedlineBook (1.4) - Representation of a MEDLINE book Bio::Biblio::JournalArticle (1.4) - Representation of a journal article Bio::Biblio::MedlineBookArticle (1.4) - Representation of a MEDLINE book article Bio::Biblio::Patent (1.4) - Representation of a patent Bio::Biblio::Service (1.4) - Representation of a provider of type service Bio::Biblio::MedlineArticle (1.4) - Representation of a MEDLINE article Bio::Biblio::PubmedArticle (1.4) - Representation of a PUBMED article Bio::Biblio::MedlineJournal (1.4) - Representation of a MEDLINE journal Bio::Biblio::Proceeding (1.4) - Representation of a conference proceeding Bio::Biblio::Book (1.4) - Representation of a book Bio::Biblio::IO::medline2ref (1.4) - A converter of a raw hash to MEDLINE citations Bio::Biblio::IO::pubmedxml (1.4) - A converter of XML files with PUBMED citations Bio::Biblio::IO::pubmed2ref (1.4) - A converter of a raw hash to PUBMED citations Bio::Biblio::IO::medlinexml (1.4) - A converter of XML files with MEDLINE citations Bio::Align::Utilities (1.4) - A collection of utilities regarding converting and manipulating alignment objects Bio::Align::AlignI (1.4) - An interface for describing sequence alignments. Bio::Align::DNAStatistics (1.4) - Calculate some statistics for a DNA alignment Bio::Align::StatisticsI (1.4) - Calculate some statistics for an alignment Bio::Align::PairwiseStatistics (1.4) - Base statistic object for Pairwise Alignments Bio::TreeIO::nexus (1.4) - A TreeIO driver module for parsing Nexus tree output from PAUP Bio::TreeIO::TreeEventBuilder (1.4) - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events Bio::TreeIO::lintree (1.4) - Parser for lintree output trees Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output Bio::TreeIO::tabtree (1.4) - A simple output format which displays a tree as an ASCII drawing Bio::TreeIO::nhx (1.4) - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. Bio::TreeIO::newick (1.4) - TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. Bio::Coordinate::Graph (1.4) - Finds shortest path between nodes in a graph Bio::Coordinate::ExtrapolatingPair (1.4) - Continuous match between two coordinate sets Bio::Coordinate::Result (1.4) - Results from coordinate transformation Bio::Coordinate::MapperI (1.4) - Interface describing coordinate mappers Bio::Coordinate::Utils (1.4) - Additional methods to create Bio::Coordinate objects Bio::Coordinate::Chain (1.4) - Mapping locations through a chain of coordinate mappers Bio::Coordinate::Collection (1.4) - Noncontinuous match between two coordinate sets Bio::Coordinate::Pair (1.4) - Continuous match between two coordinate sets Bio::Coordinate::ResultI (1.4) - Interface to identify coordinate mapper results Bio::Coordinate::GeneMapper (1.4) - transformations between gene related coordinate systems Bio::Coordinate::Result::Gap (1.4) - Another name for Bio::Location::Simple Bio::Coordinate::Result::Match (1.4) - Another name for Bio::Location::Simple Bio::Root::RootI (1.4) - Abstract interface to root object code Bio::Root::Global (1.4) - Global variables and utility functions Bio::Root::Root (1.4) - Hash-based implementation of Bio::Root::RootI Bio::Root::HTTPget (1.4) - module for fallback HTTP get operations when LWP:: is unavailable Bio::Root::Storable (1.4) - object serialisation methods Bio::Root::IOManager (1.4) - Input and output manager for Perl5 objects. Bio::Root::Version (1.4) - provide global, distribution-level versioning Bio::Root::Vector (1.4) - Interface for managing linked lists of Perl5 objects. Bio::Root::Err (1.4) - Exception class for Perl 5 objects Bio::Root::IO (1.4) - module providing several methods often needed when dealing with file IO Bio::Root::Utilities (1.4) - General-purpose utility module Bio::Root::Xref (1.4) - A generic cross-reference object. Bio::Root::Exception (1.4) - Generic exception objects for Bioperl Bio::Root::Object (1.4) - A core Perl 5 object. Bio::Location::Fuzzy (1.4) - Implementation of a Location on a Sequence which has unclear start and/or end locations Bio::Location::SplitLocationI (1.4) - Abstract interface of a Location on a Sequence which has multiple locations (start/end points) Bio::Location::Atomic (1.4) - Implementation of a Atomic Location on a Sequence Bio::Location::CoordinatePolicyI (1.4) - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location Bio::Location::AvWithinCoordPolicy (1.4) - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise Bio::Location::Simple (1.4) - Implementation of a Simple Location on a Sequence Bio::Location::Split (1.4) - Implementation of a Location on a Sequence which has multiple locations (start/end points) Bio::Location::WidestCoordPolicy (1.4) - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range Bio::Location::NarrowestCoordPolicy (1.4) - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range Bio::Location::FuzzyLocationI (1.4) - Abstract interface of a Location on a Sequence which has unclear start/end location Bio::Index::Swissprot (1.4) - Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). Bio::Index::AbstractSeq (1.4) - Base class for AbstractSeq s Bio::Index::GenBank (1.4) - Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). Bio::Index::SwissPfam (1.4) - Interface for indexing swisspfam files Bio::Index::EMBL (1.4) - Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). Bio::Index::Fasta (1.4) - Interface for indexing (multiple) fasta files Bio::Index::Fastq (1.4) - Interface for indexing (multiple) fastq files Bio::Index::Blast (1.4) - Indexes Blast reports and supports retrieval based on query accession(s) Bio::Index::Abstract (1.4) - Abstract interface for indexing a flat file Bio::Annotation::OntologyTerm (1.4) - An ontology term adapted to AnnotationI Bio::Annotation::SimpleValue (1.4) - A simple scalar Bio::Annotation::AnnotationFactory (1.4) - Instantiates a new Bio::AnnotationI (or derived class) through a factory Bio::Annotation::Reference (1.4) - Specialised DBLink object for Literature References Bio::Annotation::Collection (1.4) - Default Perl implementation of AnnotationCollectionI Bio::Annotation::DBLink (1.4) - DESCRIPTION of Object Bio::Annotation::StructuredValue (1.4) - A scalar with embedded structured information Bio::Annotation::Comment (1.4) - A comment object, holding text Bio::Annotation::TypeManager (1.4) - Manages types for annotation collections Bio::Map::SimpleMap (1.4) - A MapI implementation handling the basics of a Map Bio::Map::MappableI (1.4) - An object that can be placed in a map Bio::Map::CytoMap (1.4) - A Bio::MapI compliant map implementation handling cytogenic bands Bio::Map::PositionI (1.4) - Abstracts the notion of a position having a value in the context of a marker and a Map Bio::Map::MarkerI (1.4) - Interface for basic marker functionality Bio::Map::Position (1.4) - A single position of a Marker in a Map Bio::Map::Microsatellite (1.4) - An object representing a Microsatellite marker. Bio::Map::CytoPosition (1.4) - Marker class with cytogenetic band storing attributes Bio::Map::LinkagePosition (1.4) - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap Bio::Map::Marker (1.4) - An central map object representing a generic marker that can have multiple location in several maps. Bio::Map::LinkageMap (1.4) - A representation of a genetic linkage map. Bio::Map::MapI (1.4) - Interface for describing Map objects in bioperl Bio::Map::OrderedPosition (1.4) - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. Bio::Map::CytoMarker (1.4) - An object representing a marker. Bio::Map::OrderedPositionWithDistance (1.4) - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. Bio::Seq::BaseSeqProcessor (1.4) - Base implementation for a SequenceProcessor Bio::Seq::TraceI (1.4) - Interface definition for a Bio::Seq::Trace Bio::Seq::PrimaryQual (1.4) - Bioperl lightweight Quality Object Bio::Seq::PrimedSeq (1.4) - A representation of a sequence and two primers flanking a target region for amplification Bio::Seq::SeqFastaSpeedFactory (1.4) - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory Bio::Seq::SeqFactory (1.4) - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory Bio::Seq::LargePrimarySeq (1.4) - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root Bio::Seq::SequenceTrace (1.4) - Bioperl object packaging a sequence with its trace Bio::Seq::Meta (1.4) - Generic superclass for sequence objects with residue-based meta information Bio::Seq::QualI (1.4) - Interface definition for a Bio::Seq::Qual Bio::Seq::SeqWithQuality (1.4) - Bioperl object packaging a sequence with its quality Bio::Seq::RichSeqI (1.4) - interface for sequences from rich data sources, mostly databases Bio::Seq::RichSeq (1.4) - Module implementing a sequence created from a rich sequence database entry Bio::Seq::LargeSeq (1.4) - SeqI compliant object that stores sequence as files in /tmp Bio::Seq::EncodedSeq (1.4) - subtype of L to store DNA that encodes a protein Bio::Seq::MetaI (1.4) - Interface for sequence objects with residue-based meta information Bio::Seq::SeqBuilder (1.4) - Configurable object builder for sequence stream parsers Bio::Seq::Meta::Array (1.4) - array-based generic implementation of a sequence class with residue-based meta information Bio::Graphics::ConfiguratorI (1.4) - A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag-Evalue semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse). Bio::Graphics::Feature (1.4) - A simple feature object for use with Bio::Graphics::Panel Bio::Graphics::Pictogram (1.4) - Bio::Graphics::Pictogram Bio::Graphics::RendererI (1.4) - A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI. Bio::Graphics::FeatureFile (1.4) - A set of Bio::Graphics features, stored in a file Bio::Graphics::Panel (1.4) - Generate GD images of Bio::Seq objects Bio::Graphics::Glyph (1.4) - Base class for Bio::Graphics::Glyph objects Bio::Graphics::Glyph::segmented_keyglyph (1.4) - The "segmented_keyglyph" glyph Bio::Graphics::Glyph::box (1.4) - The "box" glyph Bio::Graphics::Glyph::cds (1.4) - The "cds" glyph Bio::Graphics::Glyph::extending_arrow (1.4) - The "extending arrow" glyph Bio::Graphics::Glyph::group (1.4) - The "group" glyph Bio::Graphics::Glyph::processed_transcript (1.4) - The sequence ontology transcript glyph Bio::Graphics::Glyph::minmax (1.4) - The minmax glyph Bio::Graphics::Glyph::generic (1.4) - The "generic" glyph Bio::Graphics::Glyph::rndrect (1.4) - The "round rect" glyph Bio::Graphics::Glyph::ex (1.4) - The "crossbox" glyph Bio::Graphics::Glyph::diamond (1.4) - The "diamond" glyph Bio::Graphics::Glyph::ellipse (1.4) - The "ellipse" glyph Bio::Graphics::Glyph::oval (1.4) - The "oval" glyph Bio::Graphics::Glyph::anchored_arrow (1.4) - The "anchored_arrow" glyph Bio::Graphics::Glyph::pinsertion (1.4) - The "Drosophila P-element Insertion" glyph Bio::Graphics::Glyph::toomany (1.4) - The "too many to show" glyph Bio::Graphics::Glyph::graded_segments (1.4) - The "graded_segments" glyph Bio::Graphics::Glyph::dna (1.4) - The "dna" glyph Bio::Graphics::Glyph::triangle (1.4) - The "triangle" glyph Bio::Graphics::Glyph::alignment (1.4) - The "alignment" glyph Bio::Graphics::Glyph::redgreen_box (1.4) - The "redgreen_box" glyph Bio::Graphics::Glyph::Factory (1.4) - Factory for Bio::Graphics::Glyph objects Bio::Graphics::Glyph::translation (1.4) - The "6-frame translation" glyph Bio::Graphics::Glyph::primers (1.4) - The "STS primers" glyph Bio::Graphics::Glyph::heterogeneous_segments (1.4) - The "heterogeneous_segments" glyph Bio::Graphics::Glyph::crossbox (1.4) - The "crossbox" glyph Bio::Graphics::Glyph::segments (1.4) - The "segments" glyph Bio::Graphics::Glyph::redgreen_segment (1.4) - The "redgreen_segments" glyph Bio::Graphics::Glyph::transcript2 (1.4) - The "transcript2" glyph Bio::Graphics::Glyph::transcript (1.4) - The "transcript" glyph Bio::Graphics::Glyph::dot (1.4) - The "dot" glyph Bio::Graphics::Glyph::xyplot (1.4) - The xyplot glyph Bio::Graphics::Glyph::arrow (1.4) - The "arrow" glyph Bio::Graphics::Glyph::ruler_arrow (1.4) - The "ruler_arrow" glyph Bio::Graphics::Glyph::track (1.4) - The "track" glyph Bio::Graphics::Glyph::line (1.4) - The "line" glyph Bio::Graphics::Glyph::splice_site (1.4) - The "splice_site" glyph Bio::Graphics::Glyph::span (1.4) - The "span" glyph Bio::Graphics::FeatureFile::Iterator - Iterator across a Bio::Graphics::FeatureFile Bio::SeqFeature::Collection (1.4) - A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. Bio::SeqFeature::Generic (1.4) - Generic SeqFeature Bio::SeqFeature::SimilarityPair (1.4) - Sequence feature based on the similarity of two sequences. Bio::SeqFeature::Similarity (1.4) - A sequence feature based on similarity Bio::SeqFeature::AnnotationAdaptor (1.4) - integrates SeqFeatureIs annotation Bio::SeqFeature::Primer (1.4) - Primer Generic SeqFeature Bio::SeqFeature::FeaturePair (1.4) - hold pair feature information e.g. blast hits Bio::SeqFeature::PositionProxy (1.4) - handle features when truncation/revcom sequences span a feature Bio::SeqFeature::CollectionI (1.4) - An interface for a collection of SeqFeatureI objects. Bio::SeqFeature::Computation (1.4) - Computation SeqFeature Bio::SeqFeature::Gene::Exon (1.4) - a feature representing an exon Bio::SeqFeature::Gene::NC_Feature (1.4) - DESCRIPTION of Object Bio::SeqFeature::Gene::TranscriptI (1.4) - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. Bio::SeqFeature::Gene::Transcript (1.4) - A feature representing a transcript Bio::SeqFeature::Gene::GeneStructureI (1.4) - A feature representing an arbitrarily complex structure of a gene Bio::SeqFeature::Gene::Poly_A_site (1.4) - DESCRIPTION of Object Bio::SeqFeature::Gene::ExonI (1.4) - Interface for a feature representing an exon Bio::SeqFeature::Gene::Promoter (1.4) - Describes a promotor Bio::SeqFeature::Gene::Intron (1.4) - DESCRIPTION of Object Bio::SeqFeature::Gene::UTR (1.4) - A feature representing an untranslated region that is part of a transcriptional unit Bio::SeqFeature::Gene::GeneStructure (1.4) - A feature representing an arbitrarily complex structure of a gene Bio::SeqFeature::Tools::TypeMapper (1.4) - maps $seq_feature-Eprimary_tag Bio::SeqFeature::Tools::Unflattener (1.4) - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy Bio::SeqFeature::SiRNA::Oligo (1.4) - Perl object for small inhibitory RNAs. Bio::SeqFeature::SiRNA::Pair (1.4) - Perl object for small inhibitory RNA (SiRNA) oligo pairs Bio::Tree::TreeI (1.4) - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. Bio::Tree::AlleleNode (1.4) - A Node with Alleles attached Bio::Tree::TreeFunctionsI (1.4) - Decorated Interface implementing basic Tree exploration methods Bio::Tree::NodeI (1.4) - Interface describing a Tree Node Bio::Tree::RandomFactory (1.4) - TreeFactory for generating Random Trees Bio::Tree::Node (1.4) - A Simple Tree Node Bio::Tree::NodeNHX (1.4) - A Simple Tree Node with support for NHX tags Bio::Tree::Tree (1.4) - An Implementation of TreeI interface. Bio::Tree::Statistics (1.4) - Calculate certain statistics for a Tree Bio::SeqIO::fastq (1.4) - fastq sequence input/output stream Bio::SeqIO::largefasta (1.4) - method i/o on very large fasta sequence files Bio::SeqIO::ctf (1.4) - ctf trace sequence input/output stream Bio::SeqIO::raw (1.4) - raw sequence file input/output stream Bio::SeqIO::metafasta (1.4) - metafasta sequence input/output stream Bio::SeqIO::qual (1.4) - .qual file input/output stream Bio::SeqIO::kegg (1.4) - KEGG sequence input/output stream Bio::SeqIO::pln (1.4) - pln trace sequence input/output stream Bio::SeqIO::locuslink (1.4) - DESCRIPTION of Object Bio::SeqIO::scf (1.4) - .scf file input/output stream Bio::SeqIO::fasta (1.4) - fasta sequence input/output stream Bio::SeqIO::phd (1.4) - .phd file input/output stream Bio::SeqIO::embl (1.4) - EMBL sequence input/output stream Bio::SeqIO::tigr (1.4) - TIGR XML sequence input/output stream Bio::SeqIO::asciitree (1.4) - asciitree sequence input/output stream Bio::SeqIO::genbank (1.4) - GenBank sequence input/output stream Bio::SeqIO::abi (1.4) - abi trace sequence input/output stream Bio::SeqIO::chadoxml (1.4) - chadoxml sequence input/output stream Bio::SeqIO::gcg (1.4) - GCG sequence input/output stream Bio::SeqIO::alf (1.4) - alf trace sequence input/output stream Bio::SeqIO::bsml - BSML sequence input/output stream Bio::SeqIO::exp (1.4) - exp trace sequence input/output stream Bio::SeqIO::swiss (1.4) - Swissprot sequence input/output stream Bio::SeqIO::FTHelper (1.4) - Helper class for Embl/Genbank feature tables Bio::SeqIO::ztr (1.4) - ztr trace sequence input/output stream Bio::SeqIO::pir (1.4) - PIR sequence input/output stream Bio::SeqIO::game (1.4) - a class for parsing and writing game-XML Bio::SeqIO::MultiFile (1.4) - Treating a set of files as a single input stream Bio::SeqIO::ace (1.4) - ace sequence input/output stream Bio::SeqIO::tab (1.4) - nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" Bio::SeqIO::game::seqHandler (1.4) - a class for handling game-XML sequences Bio::SeqIO::game::gameSubs (1.4) - a base class for game-XML parsing Bio::SeqIO::game::gameWriter (1.4) - a class for writing game-XML Bio::SeqIO::game::gameHandler (1.4) - PerlSAX handler for game-XML Bio::SeqIO::game::featHandler (1.4) - a class for handling feature elements Bio::Phenotype::Phenotype (1.4) - A class for modeling phenotypes Bio::Phenotype::Correlate (1.4) - Representation of a correlating phenotype in a given species Bio::Phenotype::PhenotypeI (1.4) - An interface for classes modeling phenotypes Bio::Phenotype::Measure (1.4) - Representation of context/value(-range)/unit triplets Bio::Phenotype::OMIM::MiniMIMentry (1.4) - Representation of a Mini MIM entry Bio::Phenotype::OMIM::OMIMparser (1.4) - parser for the OMIM database Bio::Phenotype::OMIM::OMIMentry (1.4) - represents OMIM (Online Mendelian Inheritance in Man) database entries Bio::Phenotype::OMIM::OMIMentryAllelicVariant (1.4) - Representation of a allelic variant of the OMIM database Bio::Phenotype::MeSH::Twig (1.4) - Context for a MeSH term Bio::Phenotype::MeSH::Term (1.4) - A MeSH term Bio::Variation::Allele (1.4) - Sequence object with allele-specific attributes Bio::Variation::SeqDiff (1.4) - Container class for mutation/variant descriptions Bio::Variation::RNAChange (1.4) - Sequence change class for RNA level Bio::Variation::IO (1.4) - Handler for sequence variation IO Formats Bio::Variation::AAReverseMutate (1.4) - point mutation and codon information from single amino acid changes Bio::Variation::DNAMutation (1.4) - DNA level mutation class Bio::Variation::SNP (1.4) - submitted SNP Bio::Variation::VariantI (1.4) - Sequence Change SeqFeature abstract class Bio::Variation::AAChange (1.4) - Sequence change class for polypeptides Bio::Variation::IO::xml (1.4) - XML sequence variation input/output stream Bio::Variation::IO::flat (1.4) - flat file sequence variation input/output stream Bio::Restriction::Enzyme (1.4) - A single restriction endonuclease (cuts DNA at specific locations) Bio::Restriction::IO (1.4) - Handler for sequence variation IO Formats Bio::Restriction::EnzymeI (1.4) - Interface class for restriction endonuclease Bio::Restriction::EnzymeCollection (1.4) - Set of restriction endonucleases Bio::Restriction::Analysis (1.4) - cutting sequences with restriction enzymes Bio::Restriction::Enzyme::MultiCut (1.4) - A single restriction endonuclease Bio::Restriction::Enzyme::MultiSite (1.4) - A single restriction endonuclease Bio::Restriction::IO::base (1.4) - base enzyme set Bio::Restriction::IO::itype2 (1.4) - itype2 enzyme set Bio::Restriction::IO::withrefm (1.4) - withrefm enzyme set Bio::Restriction::IO::bairoch - bairoch enzyme set Bio::Structure::Chain (1.4) - Bioperl structure Object, describes a chain Bio::Structure::StructureI (1.4) - Abstract Interface for a Structure objects Bio::Structure::Atom (1.4) - Bioperl structure Object, describes an Atom Bio::Structure::Model (1.4) - Bioperl structure Object, describes a Model Bio::Structure::IO (1.4) - Handler for Structure Formats Bio::Structure::Entry (1.4) - Bioperl structure Object, describes the whole entry Bio::Structure::Residue (1.4) - Bioperl structure Object, describes a Residue Bio::Structure::IO::pdb (1.4) - PDB input/output stream Bio::Structure::SecStr::DSSP::Res (1.4) - Module for parsing/accessing dssp output Bio::Structure::SecStr::STRIDE::Res (1.4) - Module for parsing/accessing stride output Bio::Assembly::ContigAnalysis (1.4) - Perform analysis on sequence assembly contigs. Bio::Assembly::ScaffoldI (1.4) - Abstract Inteface of Sequence Assemblies Bio::Assembly::Scaffold (1.4) - Perl module to hold and manipulate sequence assembly data. Bio::Assembly::Contig (1.4) - Perl module to hold and manipulate sequence assembly contigs. Bio::Assembly::IO (1.4) - Handler for Assembly::IO Formats Bio::Assembly::IO::phrap (1.4) - driver to load phrap.out files. Bio::Assembly::IO::ace (1.4) - module to load phrap ACE files. Bio::Event::EventHandlerI (1.4) - An Event Handler Interface Bio::Event::EventGeneratorI (1.4) - This interface describes the basic event generator class. Bio::Ontology::OntologyI (1.4) - Interface for an ontology implementation Bio::Ontology::RelationshipType (1.4) - a relationship type for an ontology Bio::Ontology::RelationshipI (1.4) - Interface for a relationship between ontology terms Bio::Ontology::TermI (1.4) - interface for ontology terms Bio::Ontology::OntologyEngineI (1.4) - Interface a minimal Ontology implementation should satisfy Bio::Ontology::Term (1.4) - interface for ontology terms Bio::Ontology::OntologyStore (1.4) - A repository of ontologies Bio::Ontology::Ontology (1.4) - standard implementation of an Ontology Bio::Ontology::SimpleOntologyEngine (1.4) - Implementation of OntologyEngineI interface Bio::Ontology::PathI (1.4) - Interface for a path between ontology terms Bio::Ontology::Relationship (1.4) - a relationship for an ontology Bio::Ontology::Path (1.4) - a path for an ontology term graph Bio::Ontology::SimpleGOEngine (1.4) - a Ontology Engine for GO implementing OntologyEngineI Bio::Ontology::InterProTerm (1.4) - Implementation of InterProI term interface Bio::Ontology::RelationshipFactory (1.4) - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory Bio::Ontology::GOterm (1.4) - representation of GO terms Bio::Ontology::TermFactory (1.4) - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory Bio::Taxonomy::Tree (1.4) - An Organism Level Implementation of TreeI interface. Bio::Taxonomy::Node (1.4) - A node in a represented taxonomy Bio::Taxonomy::FactoryI (1.4) - interface to define how to access NCBI Taxonoy Bio::Taxonomy::Taxon (1.4) - Generic Taxonomic Entity object Bio::CodonUsage::Table (1.4) - for access to the Codon usage Database at http://www.kazusa.or.jp/codon. Bio::CodonUsage::IO (1.4) - for reading and writing codon usage tables to file Bio::Symbol::AlphabetI (1.4) - A Symbol Alphabet Bio::Symbol::DNAAlphabet (1.4) - A ready made DNA alphabet Bio::Symbol::Symbol (1.4) - A biological symbol Bio::Symbol::Alphabet (1.4) - DESCRIPTION of Object Bio::Symbol::ProteinAlphabet (1.4) - A ready made Protein alphabet Bio::Symbol::SymbolI (1.4) - Interface for a Symbol Bio::OntologyIO::InterProParser (1.4) - Parser for InterPro xml files. Bio::OntologyIO::soflat (1.4) - a parser for the Sequence Ontology flat-file format Bio::OntologyIO::goflat (1.4) - a parser for the Gene Ontology flat-file format Bio::OntologyIO::simplehierarchy (1.4) - a base class parser for simple hierarchy-by-indentation type formats Bio::OntologyIO::dagflat (1.4) - a base class parser for GO flat-file type formats Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler (1.4) - Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler Bio::OntologyIO::Handlers::InterProHandler (1.4) - XML handler class for InterProParser Bio::OntologyIO::Handlers::BaseSAXHandler (1.4) - Bio::OntologyIO::Handlers::BaseSAXHandler Bio::MapIO::mapmaker (1.4) - A Mapmaker Map reader Bio::Expression::FeatureGroup (1.4) - a set of DNA/RNA features. ISA Bio::Expression::FeatureI Bio::Expression::FeatureI (1.4) - an interface class for DNA/RNA features Bio::Das::SegmentI (1.4) - DAS-style access to a feature database Bio::Das::FeatureTypeI (1.4) - Simple interface to Sequence Ontology feature types Bio::ClusterIO::unigene (1.4) - UniGene input stream Bio::ClusterIO::dbsnp (1.4) - dbSNP input stream 5.8.3::URI - Uniform Resource Identifiers (absolute and relative) 5.8.3::LWP - The World-Wide Web library for Perl 5.8.3::SVG - Perl extension for generating Scalable Vector Graphics (SVG) documents 5.8.3::Ace - Object-Oriented Access to ACEDB Databases 5.8.3::Heap - Perl extensions for keeping data partially sorted 5.8.3::Graph - graph operations 5.8.3::sun4-solaris-thread-multi::GD - Interface to Gd Graphics Library 5.8.3::sun4-solaris-thread-multi::HTML::PullParser - Alternative HTML::Parser interface 5.8.3::sun4-solaris-thread-multi::HTML::Parser - HTML parser class 5.8.3::sun4-solaris-thread-multi::HTML::Entities - Encode or decode strings with HTML entities 5.8.3::sun4-solaris-thread-multi::HTML::TokeParser - Alternative HTML::Parser interface 5.8.3::sun4-solaris-thread-multi::HTML::LinkExtor - Extract links from an HTML document 5.8.3::sun4-solaris-thread-multi::HTML::Filter - Filter HTML text through the parser 5.8.3::sun4-solaris-thread-multi::HTML::HeadParser - Parse section of a HTML document 5.8.3::sun4-solaris-thread-multi::GD::Polyline - Polyline object and Polygon utilities (including splines) for use with GD 5.8.3::sun4-solaris-thread-multi::XML::Parser - A perl module for parsing XML documents 5.8.3::sun4-solaris-thread-multi::XML::Parser::Expat - Lowlevel access to James Clark's expat XML parser 5.8.3::sun4-solaris-thread-multi::XML::Parser::Style::Tree - XML::Parser::Style::Tree 5.8.3::sun4-solaris-thread-multi::XML::Parser::Style::Subs - XML::Parser::Style::Subs 5.8.3::sun4-solaris-thread-multi::XML::Parser::Style::Objects - XML::Parser::Style::Objects 5.8.3::sun4-solaris-thread-multi::XML::Parser::Style::Debug - Debug style for XML::Parser 5.8.3::sun4-solaris-thread-multi::XML::Parser::Style::Stream - Stream style for XML::Parser 5.8.3::URI::QueryParam - Additional query methods for URIs 5.8.3::URI::WithBase - URIs which remember their base 5.8.3::URI::data - URI that contains immediate data 5.8.3::URI::ldap - LDAP Uniform Resource Locators 5.8.3::URI::Heuristic - Expand URI using heuristics 5.8.3::URI::URL - Uniform Resource Locators 5.8.3::URI::file - URI that maps to local file names 5.8.3::URI::Split - Parse and compose URI strings 5.8.3::URI::Escape - Escape and unescape unsafe characters 5.8.3::HTML::Tagset - data tables useful in parsing HTML 5.8.3::HTML::Form - Class that represents an HTML form element 5.8.3::LWP::RobotUA - a class for well-behaved Web robots 5.8.3::LWP::Protocol - Base class for LWP protocols 5.8.3::LWP::UserAgent - Web user agent class 5.8.3::LWP::MemberMixin - Member access mixin class 5.8.3::LWP::Debug - debug routines for the libwww-perl library 5.8.3::LWP::ConnCache - Connection cache manager 5.8.3::LWP::MediaTypes - guess media type for a file or a URL 5.8.3::LWP::DebugFile - routines for tracing/debugging LWP 5.8.3::LWP::Simple - simple procedural interface to LWP 5.8.3::LWP::Authen::Ntlm - Library for enabling NTLM authentication (Microsoft) in LWP 5.8.3::HTTP::Message - HTTP style message base class 5.8.3::HTTP::Status - HTTP Status code processing 5.8.3::HTTP::Daemon - a simple http server class 5.8.3::HTTP::Cookies - HTTP cookie jars 5.8.3::HTTP::Date - date conversion routines 5.8.3::HTTP::Request - HTTP style request message 5.8.3::HTTP::Negotiate - choose a variant to serve 5.8.3::HTTP::Response - HTTP style response message 5.8.3::HTTP::Headers - Class encapsulating HTTP Message headers 5.8.3::HTTP::Headers::Util - Header value parsing utility functions 5.8.3::HTTP::Request::Common - Construct common HTTP::Request objects 5.8.3::HTTP::Cookies::Netscape - access to Netscape cookies files 5.8.3::HTTP::Cookies::Microsoft - access to Microsoft cookies files 5.8.3::Net::HTTP - Low-level HTTP connection (client) 5.8.3:Net::HTTP::NB - Non-blocking HTTP client 5.8.3::File::Listing - parse directory listing 5.8.3::WWW:8.3::SVG::Element - Generate the element bits for SVG.pm 5.8.3::GD::SVG - Seamlessly enable SVG output from scripts written using GD 5.8.3::Ace::Iterator - Iterate Across an ACEDB Query 5.8.3::Ace::Local - use giface, tace or gifaceclient to open a local connection to an Ace database 5.8.3::Ace::Object - Manipulate Ace Data Objects 5.8.3::Ace::Model - Get information about AceDB models 5.8.3::Ace::Sequence - Examine ACeDB Sequence Objects 5.8.3::Ace::Graphics::GlyphFactory - Create Ace::Graphics::Glyphs 5.8.3::Ace::Graphics::Glyph - Base class for Ace::Graphics::Glyph objects 5.8.3::Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects 5.8.3::Ace::Graphics::Fk - A dummy feature object used for generating panel key tracks 5.8.3::Ace::Graphics::Panel - PNG graphics of Ace::Sequence::Feature objects 5.8.3::Ace::Graphics::Glyph::box - The "box" glyph 5.8.3::Ace::Graphics::Glyph::arrow - The "arrow" glyph 5.8.3::Ace::Graphics::Glyph::toomany - The "too many to show" glyph 5.8.3::Ace::Graphics::Glyph::primers - The "STS primers" glyph 5.8.3::Ace::Graphics::Glyph::ex - The "X" glyph 5.8.3::Ace::Graphics::Glyph::dot - The "ellipse" glyph 5.8.3::Ace::Graphics::Glyph::span - The "span" glyph 5.8.3::Ace::Graphics::Glyph::transcript - The "gene" glyph 5.8.3::Ace::Graphics::Glyph::triangle - The "triangle" glyph 5.8.3::Ace::Graphics::Glyph::line - The "line" glyph 5.8.3::Ace::Graphics::Glyph::segments - The "discontinuous segments" glyph 5.8.3::Ace::Graphics::Glyph::group - The group glyph 5.8.3::Ace::Graphics::Glyph::anchored_arrow - The "anchored_arrow" glyph 5.8.3::Ace::Graphics::Glyph::graded_segments - The "color-coded segments" glyph 5.8.3::Ace::Sequence::Gene - Simple "Gene" Object 5.8.3::Ace::Sequence::GappedAlignment - Gapped alignment object 5.8.3::Ace::Sequence::Multi - Combine Feature Tables from Multiple Databases 5.8.3::Ace::Sequence::Feature - Examine Sequence Feature Tables 5.8.3::Ace::Sequence::FeatureList - Lightweight Access to Features 5.8.3::Ace::Sequence::Transcript - Simple "Gene" Object 5.8.3::Ace::Sequence::Homol - Temporary Sequence Homology Class 5.8.3::Ace::Browser::AceSubs - Subroutines for AceBrowser 5.8.3::Ace::Browser::SiteDefs - Access to AceBrowser configuration files 5.8.3::Ace::Browser::SearchSubs - Subroutines for AceBrowser search scripts 5.8.3::IO::Lines - IO:: interface for reading/writing an array of lines 5.8.3::IO::Stringy - I/O on in-core objects like strings and arrays 5.8.3::IO::ScalarArray - IO:: interface for reading/writing an array of scalars 5.8.3::IO::Wrap - wrap raw filehandles in IO::Handle interface 5.8.3::IO::AtomicFile - write a file which is updated atomically 5.8.3::IO::Scalar - IO:: interface for reading/writing a scalar 5.8.3::IO::InnerFile - define a file inside another file 5.8.3::IO::WrapTie - wrap tieable objects in IO::Handle interface 5.8.3::IO::String - Emulate file interface for in-core strings 5.8.3::Mail::Cap - Parse mailcap files 5.8.3::Mail::Header - manipulate mail RFC822 compliant headers 5.8.3::Mail::Mailer - Simple interface to electronic mailing mechanisms 5.8.3::Mail::Send - Simple electronic mail interface 5.8.3::Mail::Filter - Filter mail through multiple subroutines 5.8.3::Mail::Field - Base class for manipulation of mail header fields 5.8.3::Mail::Internet - manipulate Internet format (RFC 822) mail messages 5.8.3::Mail::Util - mail utility functions 5.8.3::Mail::Address - Parse mail addresses 5.8.3::Mail::Field::AddrList - object representation of e-mail address lists 5.8.3::MIME::Body - the body of a MIME message 5.8.3::MIME::Entity - class for parsed-and-decoded MIME message 5.8.3::MIME::Head - MIME message header (a subclass of Mail::Header) 5.8.3::MIME::Words - deal with RFC-1522 encoded words 5.8.3::MIME::Tools - modules for parsing (and creating!) MIME entities 5.8.3::MIME::Decoder - an object for decoding the body part of a MIME stream 5.8.3::MIME::WordDecoder - decode RFC-1522 encoded words to a local representation 5.8.3::MIME::Parser - experimental class for parsing MIME streams 5.8.3::MIME::Lite - low-calorie MIME generator 5.8.3::MIME::Decoder::Gzip64 - decode a "base64" gzip stream 5.8.3::MIME::Decoder::NBit - encode/decode a "7bit" or "8bit" stream 5.8.3::MIME::Decoder::Binary - perform no encoding/decoding 5.8.3::MIME::Decoder::UU - decode a "uuencoded" stream 5.8.3::MIME::Decoder::QuotedPrint - encode/decode a "quoted-printable" stream 5.8.3::MIME::Decoder::Base64 - encode/decode a "base64" stream 5.8.3::MIME::Field::ContDisp - a "Content-disposition" field 5.8.3::MIME::Field::ContType - a "Content-type" field 5.8.3::MIME::Field::ParamVal - subclass of Mail::Field, for structured MIME fields 5.8.3::MIME::Field::ConTraEnc - a "Content-transfer-encoding" field 5.8.3::MIME::Parser::Results - results of the last entity parsed 5.8.3::MIME::Parser::Filer - manage file-output of the parser 5.8.3::MIME::Parser::Reader - a line-oriented reader for a MIME::Parser 5.8.3::SOAP::Test - Test framework for SOAP::Lite 5.8.3::SOAP::Lite - Client and server side SOAP implementation 5.8.3::SOAP::Transport::JABBER - Server/Client side JABBER support for SOAP::Lite 5.8.3::SOAP::Transport::MAILTO - Client side SMTP/sendmail support for SOAP::Lite 5.8.3::SOAP::Transport::MQ - Server/Client side MQ support for SOAP::Lite 5.8.3::SOAP::Transport::POP3 - Server side POP3 support for SOAP::Lite 5.8.3::SOAP::Transport::TCP - Server/Client side TCP support for SOAP::Lite 5.8.3::SOAP::Transport::IO - Server side IO support for SOAP::Lite 5.8.3::SOAP::Transport::HTTP - Server/Client side HTTP support for SOAP::Lite 5.8.3::SOAP::Transport::LOCAL - Client side no-transport support for SOAP::Lite 5.8.3::SOAP::Transport::FTP - Client side FTP support for SOAP::Lite 5.8.3::UDDI::Lite - Library for UDDI clients in Perl 5.8.3::XML::Twig - A perl module for processing huge XML documents in tree mode. 5.8.3::XML::Writer - Perl extension for writing XML documents. 5.8.3::XML::SAX2Perl - translate Java/CORBA style SAX methods to Perl methods 5.8.3::XML::Perl2SAX - translate Perl SAX methods to Java/CORBA style methods 5.8.3::XML::ESISParser - Perl SAX parser using nsgmls 5.8.3::XML::Parser::Lite - Lightweight regexp-based XML parser 5.8.3::XML::Parser::PerlSAX - Perl SAX parser using XML::Parser 5.8.3::XML::Handler::Subs - a PerlSAX handler base class for calling user-defined subs 5.8.3::XML::Handler::Sample - a trivial PerlSAX handler 5.8.3::XML::Handler::CanonXMLWriter - output XML in canonical XML format 5.8.3::XML::Handler::XMLWriter - a PerlSAX handler for writing readable XML 5.8.3::XML::PatAct::MatchName - A pattern module for matching element names 5.8.3::XML::PatAct::ActionTempl - An action module for 5.8.3::XML::PatAct::ToObjects - An action module for creating Perl objects 5.8.3::XML::PatAct::PatternTempl - A pattern module for 5.8.3::XML::PatAct::Amsterdam - An action module for simplistic style-sheets 5.8.3::XMLRPC::Lite - client and server implementation of XML-RPC protocol 5.8.3::XMLRPC::Test - Test framework for XMLRPC::Lite 5.8.3::XMLRPC::Transport::POP3 - Server side POP3 support for XMLRPC::Lite 5.8.3::XMLRPC::Transport::TCP - Server/Client side TCP support for XMLRPC::Lite 5.8.3::XMLRPC::Transport::HTTP - Server/Client side HTTP support for XMLRPC::Lite 5.8.3::Apache::SOAP - mod_perl-based SOAP server with minimum configuration 5.8.3::Apache::XMLRPC::Lite - mod_perl-based XML-RPC server with minimum configuration 5.8.3::Text::Shellwords - Text::Shellwords 5.8.3::Heap::Binary - a Perl extension for keeping data partially sorted 5.8.3::Heap::Binomial - a Perl extension for keeping data partially sorted 5.8.3::Heap::Elem - Perl extension for elements to be put in Heaps 5.8.3::Heap::Fibonacci - a Perl extension for keeping data partially sorted 5.8.3::Heap::Elem::Num - Perl extension for Numeric Heap Elements 5.8.3::Heap::Elem::NumRev - Perl extension for Reversed Numeric Heap Elements 5.8.3::Heap::Elem::Ref - Perl extension for Object Reference Heap Elements 5.8.3::Heap::Elem::RefRev - Perl extension for reversed Object Reverence Heap Elements 5.8.3::Heap::Elem::Str - Perl extension for String Heap Elements 5.8.3::Heap::Elem::StrRev - Perl extension for Reversed String Heap Elements 5.8.3::Graph::Directed - directed graphs 5.8.3::Graph::Base - graph base class 5.8.3::Graph::Undirected - directed graphs 5.8.3::Graph::BFS - graph breadth-first search 5.8.3::Graph::HeapElem - internal use only 5.8.3::Graph::DFS - graph depth-first search 5.8.3::Graph::Traversal - graph traversal 5.8.3::Data::Grove - support for deeply nested structures 5.8.3::Data::Grove::Parent - provide parent properties to Data::Grove objects 5.8.3::Data::Grove::Visitor - add visitor/callback methods to Data::Grove objects 5.8.3::Bio::WebAgent - A base class for Web (any protocol) access 5.8.3::Bio::TreeIO - Parser for Tree files 5.8.3::Bio::LocationI - Abstract interface of a Location on a Sequence 5.8.3::Bio::Taxonomy - representing Taxonomy. 5.8.3::Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references 5.8.3::Bio::SeqIO - Handler for SeqIO Formats 5.8.3::Bio::AnalysisI - An interface to any (local or remote) analysis tool 5.8.3::Bio::MapIO - A Map Factory object 5.8.3::Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool 5.8.3::Bio::IdCollectionI - interface for objects with multiple identifiers 5.8.3::Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates 5.8.3::Bio::Biblio - A Bibliographic Query Service module 5.8.3::Bio::AlignIO - Handler for AlignIO Formats 5.8.3::Bio::Seq - Sequence object, with features 5.8.3::Bio::DescribableI - interface for objects with human readable names and descriptions 5.8.3::Bio::RangeI - Range interface 5.8.3::Bio::OntologyIO - Parser factory for Ontology formats 5.8.3::Bio::FeatureHolderI - the base interface an object with features must implement 5.8.3::Bio::AnalysisResultI - Interface for analysis result objects 5.8.3::Bio::SeqAnalysisParserI - Sequence analysis output parser interface 5.8.3::Bio::SeqI - Abstract Interface of Sequence (with features) 5.8.3::Bio::AnalysisParserI - Generic analysis output parser interface 5.8.3::Bio::SearchIO - Driver for parsing Sequence Database Searches (Blast,FASTA,...) 5.8.3::Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object 5.8.3::Bio::AnnotationCollectionI - Interface for annotation collections 5.8.3::Bio::SeqFeatureI - Abstract interface of a Sequence Feature 5.8.3::Bio::PrimarySeq - Bioperl lightweight Sequence Object 5.8.3::Bio::AnnotationI - Annotation interface 5.8.3::Bio::Graphics - Generate GD images of Bio::Seq objects 5.8.3::Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq 5.8.3::Bio::SimpleAlign - Multiple alignments held as a set of sequences 5.8.3::Bio::ClusterIO - Handler for Cluster Formats 5.8.3::Bio::IdentifiableI - interface for objects with identifiers 5.8.3::Bio::Species - Generic species object 5.8.3::Bio::ClusterI - Cluster Interface 5.8.3::Bio::LocatableSeq - A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. 5.8.3::Bio::DasI - DAS-style access to a feature database 5.8.3::Bio::SeqUtils - Additional methods for PrimarySeq objects 5.8.3::Bio::Range - Pure perl RangeI implementation 5.8.3::Bio::Perl - Functional access to BioPerl for people who don't know objects 5.8.3::Bio::AnnotatableI - the base interface an annotatable object must implement 5.8.3::Bio::PopGen::MarkerI - A Population Genetic conceptual marker 5.8.3::Bio::PopGen::PopulationI - Interface for Populations 5.8.3::Bio::PopGen::Genotype - An implementation of a genotype which is an allele container 5.8.3::Bio::PopGen::IO - Input individual,marker,allele information 5.8.3::Bio::PopGen::Population - A population of individuals 5.8.3::Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results 5.8.3::Bio::PopGen::PopStats - A collection of methods for calculating statistics about a population or sets of populations 5.8.3::Bio::PopGen::GenotypeI - A marker and alleles for a specific individual 5.8.3::Bio::PopGen::Statistics - Population Genetics statistical tests 5.8.3::Bio::PopGen::Individual - An implementation of an Individual who has Genotype or Sequence Results 5.8.3::Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes 5.8.3::Bio::PopGen::Simulation::Coalescent - A Coalescent simulation factory 5.8.3::Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation 5.8.3::Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format 5.8.3::Bio::PopGen::IO::csv - Bio::PopGen::IO::csv -Extract individual allele data from a CSV parser 5.8.3::Bio::Matrix::MatrixI - An interface for describing a Matrix 5.8.3::Bio::Matrix::Generic - A generic matrix implementation 5.8.3::Bio::Matrix::Scoring - Object which can hold scoring matrix information 5.8.3::Bio::Matrix::IO - A factory for Matrix parsing 5.8.3::Bio::Matrix::PhylipDist - A Phylip Distance Matrix object 5.8.3::Bio::Matrix::PSM::Psm - handle combination of site matricies 5.8.3::Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies 5.8.3::Bio::Matrix::PSM::InstanceSite - A PSM site occurance 5.8.3::Bio::Matrix::PSM::IO - 5.8.3::Bio::Matrix::PSM::InstanceSiteI - 5.8.3::Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation 5.8.3::Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) 5.8.3::Bio::Matrix::PSM::SiteMatrixI - SiteMatrix interface, holds a position scoring matrix (or position weight matrix) 5.8.3::Bio::Matrix::PSM::PsmHeaderI - 5.8.3::Bio::Matrix::PSM::IO::transfac - PSM transfac parser 5.8.3::Bio::Matrix::PSM::IO::mast - PSM mast parser implementation 5.8.3::Bio::Matrix::PSM::IO::meme - PSM meme parser implementation 5.8.3::Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies 5.8.3::Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies 5.8.3::Bio::Tools::GuessSeqFormat - Module for determining the sequence format of the contents of a file, a string, or through a filehandle. 5.8.3::Bio::Tools::RepeatMasker - DESCRIPTION of Object 5.8.3::Bio::Tools::Gel - Calculates relative electrophoretic migration distances 5.8.3::Bio::Tools::SeqPattern - Bioperl object for a sequence pattern or motif 5.8.3::Bio::Tools::Prints - Parser for FingerPRINTScanII program 5.8.3::Bio::Tools::dpAlign - Perl extension to do pairwise dynamic programming sequence alignment 5.8.3::Bio::Tools::pICalculator - pICalculator 5.8.3::Bio::Tools::SeqStats - Object holding statistics for one particular sequence 5.8.3::Bio::Tools::QRNA - A Parser for qrna output 5.8.3::Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis 5.8.3::Bio::Tools::ESTScan - Results of one ESTScan run 5.8.3::Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers 5.8.3::Bio::Tools::ECnumber - representation of EC numbers 5.8.3::Bio::Tools::Pseudowise - Results of one Pseudowise run 5.8.3::Bio::Tools::Genscan - Results of one Genscan run 5.8.3::Bio::Tools::Blast - Bioperl BLAST sequence analysis object 5.8.3::Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser 5.8.3::Bio::Tools::RandomDistFunctions - A set of routines useful for generating random data in different distributions 5.8.3::Bio::Tools::Primer3 - Create input for and work with the output from the program primer3 5.8.3::Bio::Tools::Seg - parse Seg output (filter low complexity protein sequence) 5.8.3::Bio::Tools::Signalp - Bio::Tools::Signalp 5.8.3::Bio::Tools::BPbl2seq - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm. 5.8.3::Bio::Tools::WWW - Bioperl manager for web resources related to biology. 5.8.3::Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object 5.8.3::Bio::Tools::SiRNA - Perl object for designing small inhibitory RNAs. 5.8.3::Bio::Tools::Promoterwise - DESCRIPTION of Object 5.8.3::Bio::Tools::Geneid - Results of one geneid run 5.8.3::Bio::Tools::Hmmpfam - Bio::Tools::Hmmpfam 5.8.3::Bio::Tools::Grail - Results of one Grail run 5.8.3::Bio::Tools::CodonTable - Bioperl codon table object 5.8.3::Bio::Tools::AlignFactory - Base object for alignment factories 5.8.3::Bio::Tools::MZEF - Results of one MZEF run 5.8.3::Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects 5.8.3::Bio::Tools::PrositeScan - Parser for ps_scan result 5.8.3::Bio::Tools::FootPrinter - DESCRIPTION of Object 5.8.3::Bio::Tools::Coil - Bio::Tools::Coil 5.8.3::Bio::Tools::Lucy - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR 5.8.3::Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence 5.8.3::Bio::Tools::SeqAnal - Bioperl sequence analysis base class. 5.8.3::Bio::Tools::Genemark - Results of one Genemark run 5.8.3::Bio::Tools::BPpsilite - Lightweight BLAST parser for (iterated) psiblast reports 5.8.3::Bio::Tools::Profile - parse Profile output 5.8.3::Bio::Tools::Glimmer - A parser for GLIMMER gene predictions 5.8.3::Bio::Tools::RestrictionEnzyme - Bioperl object for a restriction endonuclease (cuts DNA at specific locations) 5.8.3::Bio::Tools::BPlite - Lightweight BLAST parser 5.8.3::Bio::Tools::Genewise - Results of one Genewise run 5.8.3::Bio::Tools::Genomewise - Results of one Genomewise run 5.8.3::Bio::Tools::Eponine - Results of one Eponine run 5.8.3::Bio::Tools::Tmhmm - parse TmHMM output (transmembrane HMM) 5.8.3::Bio::Tools::Blat - Bio::Tools::Blat 5.8.3::Bio::Tools::EPCR - Parse ePCR output and make features 5.8.3::Bio::Tools::pSW - pairwise Smith Waterman object 5.8.3::Bio::Tools::SeqWords - Object holding n-mer statistics for one sequence 5.8.3::Bio::Tools::Blast::Sbjct - Bioperl BLAST "Hit" object 5.8.3::Bio::Tools::Blast::HTML - Bioperl Utility module for HTML formatting Blast reports 5.8.3::Bio::Tools::Blast::HSP - Bioperl BLAST High-Scoring Segment Pair object 5.8.3::Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches 5.8.3::Bio::Tools::HMMER::Results - Object representing HMMER output results 5.8.3::Bio::Tools::HMMER::Domain - One particular domain hit from HMMER 5.8.3::Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP 5.8.3::Bio::Tools::Run::StandAloneBlast - Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast. 5.8.3::Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables 5.8.3::Bio::Tools::Analysis::SimpleAnalysisBase - abstact superclass for SimpleAnalysis implementations 5.8.3::Bio::Tools::Analysis::Protein::ELM - =head1 SYNOPSIS 5.8.3::Bio::Tools::Analysis::Protein::GOR4 - a wrapper around GOR4 protein secondary structure prediction server 5.8.3::Bio::Tools::Analysis::Protein::HNN - a wrapper around HNN protein secondary structure prediction server 5.8.3::Bio::Tools::Analysis::Protein::Sopma - a wrapper around Sopma protein secondary structure prediction server 5.8.3::Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server 5.8.3::Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server 5.8.3::Bio::Tools::Analysis::Protein::Domcut - a wrapper around Domcut server 5.8.3::Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot server 5.8.3::Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server 5.8.3::Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 5.8.3::Bio::Tools::Phylo::Molphy - DESCRIPTION of Object 5.8.3::Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML 5.8.3::Bio::Tools::Phylo::PAML::Result - A PAML result set object 5.8.3::Bio::Tools::Phylo::Molphy::Result - DESCRIPTION of Object 5.8.3::Bio::Tools::Phylo::Phylip::ProtDist - DESCRIPTION of Object 5.8.3::Bio::Tools::Sim4::Exon - A single exon determined by an alignment 5.8.3::Bio::Tools::Sim4::Results - Results of one Sim4 run 5.8.3::Bio::Tools::Primer::AssessorI - interface for assessing primer pairs 5.8.3::Bio::Tools::Primer::Feature - position of a single primer 5.8.3::Bio::Tools::Primer::Pair - two primers on left and right side 5.8.3::Bio::Tools::Primer::Assessor::Base - base class for common assessor things 5.8.3::Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of sequence based on quality. 5.8.3::Bio::Tools::Alignment::Consed - A module to work with objects from consed .ace files 5.8.3::Bio::Tools::BPlite::Sbjct - A Blast Subject (database search Hit) 5.8.3::Bio::Tools::BPlite::HSP - Blast report High Scoring Pair (HSP) 5.8.3::Bio::Tools::BPlite::Iteration - object for parsing single iteration of a PSIBLAST report 5.8.3::Bio::Tools::Prediction::Gene - a predicted gene structure feature 5.8.3::Bio::Tools::Prediction::Exon - A predicted exon feature 5.8.3::Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output 5.8.3::Bio::LiveSeq::ChainI - Double linked chain data structure 5.8.3::Bio::LiveSeq::Mutation - Mutation event descriptor class 5.8.3::Bio::LiveSeq::AARange - AARange abstract class for LiveSeq 5.8.3::Bio::LiveSeq::SeqI - Abstract sequence interface class for LiveSeq 5.8.3::Bio::LiveSeq::Repeat_Unit - Repeat_Unit class for LiveSeq 5.8.3::Bio::LiveSeq::DNA - DNA object for LiveSeq 5.8.3::Bio::LiveSeq::Transcript - Transcript class for LiveSeq 5.8.3::Bio::LiveSeq::Range - Range abstract class for LiveSeq 5.8.3::Bio::LiveSeq::Repeat_Region - Repeat_Region class for LiveSeq 5.8.3::Bio::LiveSeq::Intron - Range abstract class for LiveSeq 5.8.3::Bio::LiveSeq::Gene - Range abstract class for LiveSeq 5.8.3::Bio::LiveSeq::Translation - Translation class for LiveSeq 5.8.3::Bio::LiveSeq::Prim_Transcript - Prim_Transcript class for LiveSeq 5.8.3::Bio::LiveSeq::Exon - Range abstract class for LiveSeq 5.8.3::Bio::LiveSeq::Chain - DoubleChain DataStructure for Perl 5.8.3::Bio::LiveSeq::Mutator - Package mutating LiveSequences 5.8.3::Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq 5.8.3::Bio::LiveSeq::IO::SRS - Loader for LiveSeq from EMBL entries with SRS 5.8.3::Bio::LiveSeq::IO::BioPerl - Loader for LiveSeq from EMBL entries with BioPerl 5.8.3::Bio::AlignIO::mega - Parse and Create MEGA format data files 5.8.3::Bio::AlignIO::prodom - prodom sequence input/output stream 5.8.3::Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle) 5.8.3::Bio::AlignIO::mase - mase sequence input/output stream 5.8.3::Bio::AlignIO::phylip - PHYLIP format sequence input/output stream 5.8.3::Bio::AlignIO::maf - Multipla Alignment Format sequence input stream 5.8.3::Bio::AlignIO::pfam - pfam sequence input/output stream 5.8.3::Bio::AlignIO::nexus - NEXUS format sequence input/output stream 5.8.3::Bio::AlignIO::bl2seq - bl2seq sequence input/output stream 5.8.3::Bio::AlignIO::msf - msf sequence input/output stream 5.8.3::Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files 5.8.3::Bio::AlignIO::clustalw - clustalw sequence input/output stream 5.8.3::Bio::AlignIO::fasta - FastA MSA Sequence input/output stream 5.8.3::Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream 5.8.3::Bio::AlignIO::stockholm - stockholm sequence input/output stream 5.8.3::Bio::AlignIO::meme - meme sequence input/output stream 5.8.3::Bio::AlignIO::selex - selex sequence input/output stream 5.8.3::Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory 5.8.3::Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers 5.8.3::Bio::Factory::LocationFactoryI - DESCRIPTION of Interface 5.8.3::Bio::Factory::DriverFactory - Base class for factory classes loading drivers 5.8.3::Bio::Factory::ObjectFactoryI - A General object creator factory 5.8.3::Bio::Factory::HitFactoryI - Interface for an object that builds Bio::Search::Hit::HitI objects 5.8.3::Bio::Factory::ApplicationFactoryI - Interface class for Application Factories 5.8.3::Bio::Factory::FTLocationFactory - A FeatureTable Location Parser 5.8.3::Bio::Factory::SequenceProcessorI - Interface for chained sequence processing algorithms 5.8.3::Bio::Factory::MapFactoryI - A Factory for getting markers 5.8.3::Bio::Factory::AnalysisI - An interface to analysis tool factory 5.8.3::Bio::Factory::ObjectBuilderI - Interface for an object builder 5.8.3::Bio::Factory::ResultFactoryI - Interface for an object that builds Bio::Search::Result::ResultI objects 5.8.3::Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO) 5.8.3::Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream. 5.8.3::Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers 5.8.3::Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees from/to a data stream 5.8.3::Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports (format 0) 5.8.3::Bio::SearchIO::fasta - A SearchIO parser for FASTA results 5.8.3::Bio::SearchIO::blasttable - Driver module for SearchIO for parsing NCBI -m 8/9 format 5.8.3::Bio::SearchIO::wise - Parsing of wise output as alignments 5.8.3::Bio::SearchIO::hmmer - A parser for HMMER output (hmmpfam, hmmsearch) 5.8.3::Bio::SearchIO::psl - A parser for PSL output (UCSC) 5.8.3::Bio::SearchIO::axt - a parser for axt format reports 5.8.3::Bio::SearchIO::sim4 - parser for Sim4 alignments 5.8.3::Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program alignment output 5.8.3::Bio::SearchIO::exonerate - parser for Exonerate 5.8.3::Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events. 5.8.3::Bio::SearchIO::blast - Event generator for event based parsing of blast reports 5.8.3::Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events. 5.8.3::Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing 5.8.3::Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results 5.8.3::Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for SearchIO events. 5.8.3::Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing. 5.8.3::Bio::SearchIO::Writer::HSPTableWriter - Tab-delimited data for Bio::Search::HSP::HSPI objects 5.8.3::Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format 5.8.3::Bio::SearchIO::Writer::BSMLResultWriter - DESCRIPTION of Object 5.8.3::Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each Bio::Search::Result::ResultI object. 5.8.3::Bio::SearchIO::Writer::HitTableWriter - Tab-delimited data for Bio::Search::Hit::HitI objects 5.8.3::Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text. 5.8.3::Bio::SearchIO::Writer::HTMLResultWriter - Object to implement writing a Bio::Search::ResultI in HTML. 5.8.3::Bio::DB::Flat - Interface for indexed flat files 5.8.3::Bio::DB::SwissProt - Database object interface to SwissProt retrieval 5.8.3::Bio::DB::BiblioI - An interface to a Bibliographic Query Service 5.8.3::Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs 5.8.3::Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences. 5.8.3::Bio::DB::RefSeq - Database object interface for RefSeq retrieval 5.8.3::Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases. 5.8.3::Bio::DB::Fasta - Fast indexed access to a directory of fasta files 5.8.3::Bio::DB::RandomAccessI - Abstract interface for a sequence database 5.8.3::Bio::DB::BioFetch - Database object interface to BioFetch retrieval 5.8.3::Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences 5.8.3::Bio::DB::SeqI - Abstract Interface for Sequence databases 5.8.3::Bio::DB::GenBank - Database object interface to GenBank 5.8.3::Bio::DB::MeSH - Term retrieval from a Web MeSH database 5.8.3::Bio::DB::EMBL - Database object interface for EMBL entry retrieval 5.8.3::Bio::DB::DBFetch - Database object for retrieving using the dbfetch script 5.8.3::Bio::DB::Taxonomy - Access to a taxonomy database 5.8.3::Bio::DB::Ace - Database object interface to ACeDB servers 5.8.3::Bio::DB::QueryI - Object Interface to queryable sequence databases 5.8.3::Bio::DB::InMemoryCache - Abstract interface for a sequence database 5.8.3::Bio::DB::FileCache - In file cache for BioSeq objects 5.8.3::Bio::DB::XEMBL - Database object interface for XEMBL entry retrieval 5.8.3::Bio::DB::XEMBLService - SOAP service definition for XEMBL 5.8.3::Bio::DB::CUTG - for access to the Codon usage Database at http://www.kazusa.or.jp/codon. 5.8.3::Bio::DB::Universal - Artificial database that delegates to specific databases 5.8.3::Bio::DB::GFF - Storage and retrieval of sequence annotation data 5.8.3::Bio::DB::GDB - Database object interface to GDB HTTP query 5.8.3::Bio::DB::Registry - Access to the Open Bio Database Access registry scheme 5.8.3::Bio::DB::GenPept - Database object interface to GenPept 5.8.3::Bio::DB::GFF::Feature - A relative segment identified by a feature type 5.8.3::Bio::DB::GFF::Typename - The name of a feature type 5.8.3::Bio::DB::GFF::Homol - A segment of DNA that is homologous to another 5.8.3::Bio::DB::GFF::Segment - Simple DNA segment object 5.8.3::Bio::DB::GFF::Featname - The name of a feature 5.8.3::Bio::DB::GFF::Aggregator - Aggregate GFF groups into composite features 5.8.3::Bio::DB::GFF::RelSegment - Sequence segment with relative coordinate support 5.8.3::Bio::DB::GFF::Aggregator::ucsc_unigene - UCSC UniGene aggregator 5.8.3::Bio::DB::GFF::Aggregator::ucsc_acembly - UCSC acembly aggregator 5.8.3::Bio::DB::GFF::Aggregator::ucsc_sanger22 - UCSC sanger22 aggregator 5.8.3::Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo - UCSC sanger22pseudo aggregator 5.8.3::Bio::DB::GFF::Aggregator::alignment - Alignment aggregator 5.8.3::Bio::DB::GFF::Aggregator::match - Match aggregator 5.8.3::Bio::DB::GFF::Aggregator::ucsc_softberry - UCSC softberry aggregator 5.8.3::Bio::DB::GFF::Aggregator::ucsc_twinscan - UCSC twinscan aggregator 5.8.3::Bio::DB::GFF::Aggregator::transcript - Transcript aggregator 5.8.3::Bio::DB::GFF::Aggregator::none - No aggregation 5.8.3::Bio::DB::GFF::Aggregator::ucsc_refgene - UCSC refGene aggregator 5.8.3::Bio::DB::GFF::Aggregator::clone - Clone aggregator 5.8.3::Bio::DB::GFF::Aggregator::coding - The Coding Region Aggregator 5.8.3::Bio::DB::GFF::Aggregator::ucsc_genscan - UCSC genscan aggregator 5.8.3::Bio::DB::GFF::Aggregator::processed_transcript - Sequence Ontology Transcript 5.8.3::Bio::DB::GFF::Aggregator::ucsc_ensgene - UCSC ensGene aggregator 5.8.3::Bio::DB::GFF::Adaptor::memory - Database adaptor for a specific mysql schema 5.8.3::Bio::DB::GFF::Adaptor::memory_iterator - iterator for Bio::DB::GFF::Adaptor::memory 5.8.3::Bio::DB::GFF::Adaptor::dbi - Database adaptor for DBI (SQL) databases 5.8.3::Bio::DB::GFF::Adaptor::biofetch_oracle - Cache BioFetch objects in a Bio::DB::GFF database 5.8.3::Bio::DB::GFF::Adaptor::biofetch - Cache BioFetch objects in a Bio::DB::GFF database 5.8.3::Bio::DB::GFF::Adaptor::ace - ace interface (for multiple inheritance) 5.8.3::Bio::DB::GFF::Adaptor::dbi::caching_handle - Cache for database handles 5.8.3::Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema 5.8.3::Bio::DB::GFF::Adaptor::dbi::mysql - Database adaptor for a specific mysql schema 5.8.3::Bio::DB::GFF::Adaptor::dbi::mysqlopt - Deprecated database adaptor 5.8.3::Bio::DB::GFF::Adaptor::dbi::mysqlace - Unholy union between mysql GFF database and acedb database 5.8.3::Bio::DB::GFF::Adaptor::dbi::iterator - iterator for Bio::DB::GFF::Adaptor::dbi 5.8.3::Bio::DB::GFF::Adaptor::dbi::oracleace - Unholy union between oracle GFF database and acedb database 5.8.3::Bio::DB::GFF::Adaptor::dbi::oacle - Database adaptor for a specific oracle schema 5.8.3::Bio::DB::GFF::Util::Rearrange - rearrangeface for BioHackathon standard BDB-indexed flat file 5.8.3::Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files 5.8.3::Bio::DB::Flat::BDB::swiss - swissprot adaptor for Open-bio standard BDB-indexed flat file 5.8.3::Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file 5.8.3::Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file 5.8.3::Bio::DB::Flat::BDB::swissprot - swissprot adaptor for Open-bio standard BDB-indexed flat file 5.8.3::Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file 5.8.3::Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver 5.8.3::Bio::DB::Taxonomy::flatfile - An implementation of Bio::DB::Taxonomy which uses local flat files 5.8.3::Bio::Search::Processor - DESCRIPTION of Object 5.8.3::Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects 5.8.3::Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI 5.8.3::Bio::Search::SearchUtils - Utility functions for Bio::Search:: objects 5.8.3::Bio::Search::DatabaseI - Interface for a database used in a sequence search 5.8.3::Bio::Search::HSP::PSLHSP - A HSP for PSL output 5.8.3::Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments 5.8.3::Bio::Search::HSP::PsiBlastHSP - Bioperl BLAST High-Scoring Pair object 5.8.3::Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data 5.8.3::Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair 5.8.3::Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects 5.8.3::Bio::Search::HSP::HMMERHSP - A HSP object for HMMER results 5.8.3::Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result 5.8.3::Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object 5.8.3::Bio::Search::Hit::PsiBlastHit - Bioperl BLAST Hit object 5.8.3::Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects 5.8.3::Bio::Search::Hit::HitI - Interface for a hit in a similarity search result 5.8.3::Bio::Search::Hit::BlastHit - Blast-specific subclass of Bio::Search::Hit::GenericHit 5.8.3::Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits 5.8.3::Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface 5.8.3::Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits 5.8.3::Bio::Search::Result::HMMERResult - A Result object for HMMER results 5.8.3::Bio::Search::Result::ResultI - Abstract interface to Search Result objects 5.8.3::Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult 5.8.3::Bio::Search::Result::WABAResult - Result object for WABA alignment output 5.8.3::Bio::Search::Result::ResultFactory - A factory to create Bio::Search::Result::ResultI objects 5.8.3::Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. 5.8.3::Bio::Search::Iteration::GenericIteration - A generic implementation of the Bio::Search::Iteration::IterationI interface. 5.8.3::Bio::Search::Iteration::IterationI - Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. 5.8.3::Bio::Cluster::UniGeneI - abstract interface of UniGene object 5.8.3::Bio::Cluster::UniGene - UniGene object 5.8.3::Bio::Cluster::FamilyI - Family Interface 5.8.3::Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory 5.8.3::Bio::Cluster::SequenceFamily - Sequence Family object 5.8.3::Bio::Biblio::PubmedBookArticle - Representation of a PUBMED book article 5.8.3::Bio::Biblio::Provider - Representation of a general provider 5.8.3::Bio::Biblio::BiblioBase - An abstract base for other biblio classes 5.8.3::Bio::Biblio::IO - Handling the bibliographic references 5.8.3::Bio::Biblio::Thesis - Representation of thesis 5.8.3::Bio::Biblio::Article - Representation of a general article 5.8.3::Bio::Biblio::Organisation - Representation of an organisation 5.8.3::Bio::Biblio::MedlineJournalArticle - Representation of a MEDLINE journal article 5.8.3::Bio::Biblio::BookArticle - Representation of a book article 5.8.3::Bio::Biblio::Journal - Representation of a journal 5.8.3::Bio::Biblio::PubmedJournalArticle - Representation of a PUBMED journal article 5.8.3::Bio::Biblio::Ref - Representation of a bibliographic reference 5.8.3::Bio::Biblio::TechReport - Representation of a technical report 5.8.3::Bio::Biblio::Person - Representation of a person 5.8.3::Bio::Biblio::WebResource - Representation of a web resource 5.8.3::Bio::Biblio::MedlineBook - Representation of a MEDLINE book 5.8.3::Bio::Biblio::JournalArticle - Representation of a journal article 5.8.3::Bio::Biblio::MedlineBookArticle - Representation of a MEDLINE book article 5.8.3::Bio::Biblio::Patent - Representation of a patent 5.8.3::Bio::Biblio::Service - Representation of a provider of type service 5.8.3::Bio::Biblio::MedlineArticle - Representation of a MEDLINE article 5.8.3::Bio::Biblio::PubmedArticle - Representation of a PUBMED article 5.8.3::Bio::Biblio::MedlineJournal - Representation of a MEDLINE journal 5.8.3::Bio::Biblio::Proceeding - Representation of a conference proceeding 5.8.3::Bio::Biblio::Book - Representation of a book 5.8.3::Bio::Biblio::IO::medline2ref - A converter of a raw hash to MEDLINE citations 5.8.3::Bio::Biblio::IO::pubmedxml - A converter of XML files with PUBMED citations 5.8.3::Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations 5.8.3::Bio::Biblio::IO::medlinexml - A converter of XML files with MEDLINE citations 5.8.3::Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects 5.8.3::Bio::Align::AlignI - An interface for describing sequence alignments. 5.8.3::Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment 5.8.3::Bio::Align::StatisticsI - Calculate some statistics for an alignment 5.8.3::Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments 5.8.3::Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP 5.8.3::Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events 5.8.3::Bio::TreeIO::lintree - Parser for lintree output trees 5.8.3::Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output 5.8.3::Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing 5.8.3::Bio::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. 5.8.3::Bio::TreeIO::newick - TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. 5.8.3::Bio::Coordinate::Graph - Finds shortest path between nodes in a graph 5.8.3::Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets 5.8.3::Bio::Coordinate::Result - Results from coordinate transformation 5.8.3::Bio::Coordinate::MapperI - Interface describing coordinate mappers 5.8.3::Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects 5.8.3::Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers 5.8.3::Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets 5.8.3::Bio::Coordinate::Pair - Continuous match between two coordinate sets 5.8.3::Bio::Coordinate::ResultI - Interface to identify coordinate mapper results 5.8.3::Bio::Coordinate::GeneMapper - transformations between gene related coordinate systems 5.8.3::Bio::Coordinate::Result::Gap - Another name for Bio::Location::Simple 5.8.3::Bio::Coordinate::Result::Match - Another name for Bio::Location::Simple 5.8.3::Bio::Root::RootI - Abstract interface to root object code 5.8.3::Bio::Root::Global - Global variables and utility functions 5.8.3::Bio::Root::Root - Hash-based implementation of Bio::Root::RootI 5.8.3::Bio::Root::HTTPget - module for fallback HTTP get operations when LWP:: is unavailable 5.8.3::Bio::Root::Storable - object serialisation methods 5.8.3::Bio::Root::IOManager - Input and output manager for Perl5 objects. 5.8.3::Bio::Root::Version - provide global, distribution-level versioning 5.8.3::Bio::Root::Vector - Interface for managing linked lists of Perl5 objects. 5.8.3::Bio::Root::Err - Exception class for Perl 5 objects 5.8.3::Bio::Root::IO - module providing several methods often needed when dealing with file IO 5.8.3::Bio::Root::Utilities - General-purpose utility module 5.8.3::Bio::Root::Xref - A generic cross-reference object. 5.8.3::Bio::Root::Exception - Generic exception objects for Bioperl 5.8.3::Bio::Root::Object - A core Perl 5 object. 5.8.3::Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations 5.8.3::Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points) 5.8.3::Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence 5.8.3::Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location 5.8.3::Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise 5.8.3::Bio::Location::Simple - Implementation of a Simple Location on a Sequence 5.8.3::Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points) 5.8.3::Bio::Location::WidestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range 5.8.3::Bio::Location::NarrowestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range 5.8.3::Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location 5.8.3::Bio::Index::Swissprot - Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). 5.8.3::Bio::Index::AbstractSeq - Base class for AbstractSeq s 5.8.3::Bio::Index::GenBank - Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). 5.8.3::Bio::Index::SwissPfam - Interface for indexing swisspfam files 5.8.3::Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). 5.8.3::Bio::Index::Fasta - Interface for indexing (multiple) fasta files 5.8.3::Bio::Index::Fastq - Interface for indexing (multiple) fastq files 5.8.3::Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s) 5.8.3::Bio::Index::Abstract - Abstract interface for indexing a flat file 5.8.3::Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI 5.8.3::Bio::Annotation::SimpleValue - A simple scalar 5.8.3::Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory 5.8.3::Bio::Annotation::Reference - Specialised DBLink object for Literature References 5.8.3::Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI 5.8.3::Bio::Annotation::DBLink - DESCRIPTION of Object 5.8.3::Bio::Annotation::StructuredValue - A scalar with embedded structured information 5.8.3::Bio::Annotation::Comment - A comment object, holding text 5.8.3::Bio::Annotation::TypeManager - Manages types for annotation collections 5.8.3::Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map 5.8.3::Bio::Map::MappableI - An object that can be placed in a map 5.8.3::Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands 5.8.3::Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map 5.8.3::Bio::Map::MarkerI - Interface for basic marker functionality 5.8.3::Bio::Map::Position - A single position of a Marker in a Map 5.8.3::Bio::Map::Microsatellite - An object representing a Microsatellite marker. 5.8.3::Bio::Map::CytoPosition - Marker class with cytogenetic band storing attributes 5.8.3::Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap 5.8.3::Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps. 5.8.3::Bio::Map::LinkageMap - A representation of a genetic linkage map. 5.8.3::Bio::Map::MapI - Interface for describing Map objects in bioperl 5.8.3::Bio::Map::OrderedPosition - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. 5.8.3::Bio::Map::CytoMarker - An object representing a marker. 5.8.3::Bio::Map::OrderedPositionWithDistance - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. 5.8.3::Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor 5.8.3::Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace 5.8.3::Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object 5.8.3::Bio::Seq::PrimedSeq - A representation of a sequence and two primers flanking a target region for amplification 5.8.3::Bio::Seq::SeqFastaSpeedFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory 5.8.3::Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory 5.8.3::Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root 5.8.3::Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace 5.8.3::Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information 5.8.3::Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual 5.8.3::Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality 5.8.3::Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases 5.8.3::Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry 5.8.3::Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp 5.8.3::Bio::Seq::EncodedSeq - subtype of L to store DNA that encodes a protein 5.8.3::Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information 5.8.3::Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers 5.8.3::Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information 5.8.3::Bio::Graphics::ConfiguratorI - A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag-Evalue semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse). 5.8.3::Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel 5.8.3::Bio::Graphics::Pictogram - Bio::Graphics::Pictogram 5.8.3::Bio::Graphics::RendererI - A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI. 5.8.3::Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file 5.8.3::Bio::Graphics::Panel - Generate GD images of Bio::Seq objects 5.8.3::Bio::Graphics::Glyph - Base class for Bio::Graphics::Glyph objects 5.8.3::Bio::Graphics::Glyph::segmented_keyglyph - The "segmented_keyglyph" glyph 5.8.3::Bio::Graphics::Glyph::box - The "box" glyph 5.8.3::Bio::Graphics::Glyph::cds - The "cds" glyph 5.8.3::Bio::Graphics::Glyph::extending_arrow - The "extending arrow" glyph 5.8.3::Bio::Graphics::Glyph::group - The "group" glyph 5.8.3::Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph 5.8.3::Bio::Graphics::Glyph::minmax - The minmax glyph 5.8.3::Bio::Graphics::Glyph::generic - The "generic" glyph 5.8.3::Bio::Graphics::Glyph::rndrect - The "round rect" glyph 5.8.3::Bio::Graphics::Glyph::ex - The "crossbox" glyph 5.8.3::Bio::Graphics::Glyph::diamond - The "diamond" glyph 5.8.3::Bio::Graphics::Glyph::ellipse - The "ellipse" glyph 5.8.3::Bio::Graphics::Glyph::oval - The "oval" glyph 5.8.3::Bio::Graphics::Glyph::anchored_arrow - The "anchored_arrow" glyph 5.8.3::Bio::Graphics::Glyph::pinsertion - The "Drosophila P-element Insertion" glyph 5.8.3::Bio::Graphics::Glyph::toomany - The "too many to show" glyph 5.8.3::Bio::Graphics::Glyph::graded_segments - The "graded_segments" glyph 5.8.3::Bio::Graphics::Glyph::dna - The "dna" glyph 5.8.3::Bio::Graphics::Glyph::triangle - The "triangle" glyph 5.8.3::Bio::Graphics::Glyph::alignment - The "alignment" glyph 5.8.3::Bio::Graphics::Glyph::redgreen_box - The "redgreen_box" glyph 5.8.3::Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects 5.8.3::Bio::Graphics::Glyph::translation - The "6-frame translation" glyph 5.8.3::Bio::Graphics::Glyph::primers - The "STS primers" glyph 5.8.3::Bio::Graphics::Glyph::heterogeneous_segments - The "heterogeneous_segments" glyph 5.8.3::Bio::Graphics::Glyph::crossbox - The "crossbox" glyph 5.8.3::Bio::Graphics::Glyph::segments - The "segments" glyph 5.8.3::Bio::Graphics::Glyph::redgreen_segment - The "redgreen_segments" glyph 5.8.3::Bio::Graphics::Glyph::transcript2 - The "transcript2" glyph 5.8.3::Bio::Graphics::Glyph::transcript - The "transcript" glyph 5.8.3::Bio::Graphics::Glyph::dot - The "dot" glyph 5.8.3::Bio::Graphics::Glyph::xyplot - The xyplot glyph 5.8.3::Bio::Graphics::Glyph::arrow - The "arrow" glyph 5.8.3::Bio::Graphics::Glyph::ruler_arrow - The "ruler_arrow" glyph 5.8.3::Bio::Graphics::Glyph::track - The "track" glyph 5.8.3::Bio::Graphics::Glyph::line - The "line" glyph 5.8.3::Bio::Graphics::Glyph::splice_site - The "splice_site" glyph 5.8.3::Bio::Graphics::Glyph::span - The "span" glyph 5.8.3::Bio::Graphics::FeatureFile::Iterator - Iterator across a Bio::Graphics::FeatureFile 5.8.3::Bio::SeqFeature::Collection - A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. 5.8.3::Bio::SeqFeature::Generic - Generic SeqFeature 5.8.3::Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences. 5.8.3::Bio::SeqFeature::Similarity - A sequence feature based on similarity 5.8.3::Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation 5.8.3::Bio::SeqFeature::Primer - Primer Generic SeqFeature 5.8.3::Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits 5.8.3::Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature 5.8.3::Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects. 5.8.3::Bio::SeqFeature::Computation - Computation SeqFeature 5.8.3::Bio::SeqFeature::Gene::Exon - a feature representing an exon 5.8.3::Bio::SeqFeature::Gene::NC_Feature - DESCRIPTION of Object 5.8.3::Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. 5.8.3::Bio::SeqFeature::Gene::Transcript - A feature representing a transcript 5.8.3::Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene 5.8.3::Bio::SeqFeature::Gene::Poly_A_site - DESCRIPTION of Object 5.8.3::Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon 5.8.3::Bio::SeqFeature::Gene::Promoter - Describes a promotor 5.8.3::Bio::SeqFeature::Gene::Intron - DESCRIPTION of Object 5.8.3::Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region that is part of a transcriptional unit 5.8.3::Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene 5.8.3::Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature-Eprimary_tag 5.8.3::Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy 5.8.3::Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs. 5.8.3::Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs 5.8.3::Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. 5.8.3::Bio::Tree::AlleleNode - A Node with Alleles attached 5.8.3::Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods 5.8.3::Bio::Tree::NodeI - Interface describing a Tree Node 5.8.3::Bio::Tree::RandomFactory - TreeFactory for generating Random Trees 5.8.3::Bio::Tree::Node - A Simple Tree Node 5.8.3::Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags 5.8.3::Bio::Tree::Tree - An Implementation of TreeI interface. 5.8.3::Bio::Tree::Statistics - Calculate certain statistics for a Tree 5.8.3::Bio::SeqIO::fastq - fastq sequence input/output stream 5.8.3::Bio::SeqIO::largefasta - method i/o on very large fasta sequence files 5.8.3::Bio::SeqIO::ctf - ctf trace sequence input/output stream 5.8.3::Bio::SeqIO::raw - raw sequence file input/output stream 5.8.3::Bio::SeqIO::metafasta - metafasta sequence input/output stream 5.8.3::Bio::SeqIO::qual - .qual file input/output stream 5.8.3::Bio::SeqIO::kegg - KEGG sequence input/output stream 5.8.3::Bio::SeqIO::pln - pln trace sequence input/output stream 5.8.3::Bio::SeqIO::locuslink - DESCRIPTION of Object 5.8.3::Bio::SeqIO::scf - .scf file input/output stream 5.8.3::Bio::SeqIO::fasta - fasta sequence input/output stream 5.8.3::Bio::SeqIO::phd - .phd file input/output stream 5.8.3::Bio::SeqIO::embl - EMBL sequence input/output stream 5.8.3::Bio::SeqIO::tigr - TIGR XML sequence input/output stream 5.8.3::Bio::SeqIO::asciitree - asciitree sequence input/output stream 5.8.3::Bio::SeqIO::genbank - GenBank sequence input/output stream 5.8.3::Bio::SeqIO::abi - abi trace sequence input/output stream 5.8.3::Bio::SeqIO::chadoxml - chadoxml sequence input/output stream 5.8.3::Bio::SeqIO::gcg - GCG sequence input/output stream 5.8.3::Bio::SeqIO::alf - alf trace sequence input/output stream 5.8.3::Bio::SeqIO::bsml - BSML sequence input/output stream 5.8.3::Bio::SeqIO::exp - exp trace sequence input/output stream 5.8.3::Bio::SeqIO::swiss - Swissprot sequence input/output stream 5.8.3::Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables 5.8.3::Bio::SeqIO::ztr - ztr trace sequence input/output stream 5.8.3::Bio::SeqIO::pir - PIR sequence input/output stream 5.8.3::Bio::SeqIO::game - a class for parsing and writing game-XML 5.8.3::Bio::SeqIO::MultiFile - Treating a set of files as a single input stream 5.8.3::Bio::SeqIO::ace - ace sequence input/output stream 5.8.3::Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" 5.8.3::Bio::SeqIO::game::seqHandler - a class for handling game-XML sequences 5.8.3::Bio::SeqIO::game::gameSubs - a base class for game-XML parsing 5.8.3::Bio::SeqIO::game::gameWriter - a class for writing game-XML 5.8.3::Bio::SeqIO::game::gameHandler - PerlSAX handler for game-XML 5.8.3::Bio::SeqIO::game::featHandler - a class for handling feature elements 5.8.3::Bio::Phenotype::Phenotype - A class for modeling phenotypes 5.8.3::Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species 5.8.3::Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes 5.8.3::Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets 5.8.3::Bio::Phenotype::OMIM::MiniMIMentry - Representation of a Mini MIM entry 5.8.3::Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database 5.8.3::Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries 5.8.3::Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database 5.8.3::Bio::Phenotype::MeSH::Twig - Context for a MeSH term 5.8.3::Bio::Phenotype::MeSH::Term - A MeSH term 5.8.3::Bio::Variation::Allele - Sequence object with allele-specific attributes 5.8.3::Bio::Variation::SeqDiff - Container class for mutation/variant descriptions 5.8.3::Bio::Variation::RNAChange - Sequence change class for RNA level 5.8.3::Bio::Variation::IO - Handler for sequence variation IO Formats 5.8.3::Bio::Variation::AAReverseMutate - point mutation and codon information from single amino acid changes 5.8.3::Bio::Variation::DNAMutation - DNA level mutation class 5.8.3::Bio::Variation::SNP - submitted SNP 5.8.3::Bio::Variation::VariantI - Sequence Change SeqFeature abstract class 5.8.3::Bio::Variation::AAChange - Sequence change class for polypeptides 5.8.3::Bio::Variation::IO::xml - XML sequence variation input/output stream 5.8.3::Bio::Variation::IO::flat - flat file sequence variation input/output stream 5.8.3::Bio::Restriction::Enzyme - A single restriction endonuclease (cuts DNA at specific locations) 5.8.3::Bio::Restriction::IO - Handler for sequence variation IO Formats 5.8.3::Bio::Restriction::EnzymeI - Interface class for restriction endonuclease 5.8.3::Bio::Restriction::EnzymeCollection - Set of restriction endonucleases 5.8.3::Bio::Restriction::Analysis - cutting sequences with restriction enzymes 5.8.3::Bio::Restriction::Enzyme::MultiCut - A single restriction endonuclease 5.8.3::Bio::Restriction::Enzyme::MultiSite - A single restriction endonuclease 5.8.3::Bio::Restriction::IO::base - base enzyme set 5.8.3::Bio::Restriction::IO::itype2 - itype2 enzyme set 5.8.3::Bio::Restriction::IO::withrefm - withrefm enzyme set 5.8.3::Bio::Restriction::IO::bairoch - bairoch enzyme set 5.8.3::Bio::Structure::Chain - Bioperl structure Object, describes a chain 5.8.3::Bio::Structure::StructureI - Abstract Interface for a Structure objects 5.8.3::Bio::Structure::Atom - Bioperl structure Object, describes an Atom 5.8.3::Bio::Structure::Model - Bioperl structure Object, describes a Model 5.8.3::Bio::Structure::IO - Handler for Structure Formats 5.8.3::Bio::Structure::Entry - Bioperl structure Object, describes the whole entry 5.8.3::Bio::Structure::Residue - Bioperl structure Object, describes a Residue 5.8.3::Bio::Structure::IO::pdb - PDB input/output stream 5.8.3::Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output 5.8.3::Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output 5.8.3::Bio::Assembly::ContigAnalysis - Perform analysis on sequence assembly contigs. 5.8.3::Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies 5.8.3::Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly data. 5.8.3::Bio::Assembly::Contig - Perl module to hold and manipulate sequence assembly contigs. 5.8.3::Bio::Assembly::IO - Handler for Assembly::IO Formats 5.8.3::Bio::Assembly::IO::phrap - driver to load phrap.out files. 5.8.3::Bio::Assembly::IO::ace - module to load phrap ACE files. 5.8.3::Bio::Event::EventHandlerI - An Event Handler Interface 5.8.3::Bio::Event::EventGeneratorI - This interface describes the basic event generator class. 5.8.3::Bio::Ontology::OntologyI - Interface for an ontology implementation 5.8.3::Bio::Ontology::RelationshipType - a relationship type for an ontology 5.8.3::Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms 5.8.3::Bio::Ontology::TermI - interface for ontology terms 5.8.3::Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy 5.8.3::Bio::Ontology::Term - interface for ontology terms 5.8.3::Bio::Ontology::OntologyStore - A repository of ontologies 5.8.3::Bio::Ontology::Ontology - standard implementation of an Ontology 5.8.3::Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface 5.8.3::Bio::Ontology::PathI - Interface for a path between ontology terms 5.8.3::Bio::Ontology::Relationship - a relationship for an ontology 5.8.3::Bio::Ontology::Path - a path for an ontology term graph 5.8.3::Bio::Ontology::SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI 5.8.3::Bio::Ontology::InterProTerm - Implementation of InterProI term interface 5.8.3::Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory 5.8.3::Bio::Ontology::GOterm - representation of GO terms 5.8.3::Bio::Ontology::TermFactory - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory 5.8.3::Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface. 5.8.3::Bio::Taxonomy::Node - A node in a represented taxonomy 5.8.3::Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy 5.8.3::Bio::Taxonomy::Taxon - Generic Taxonomic Entity object 5.8.3::Bio::CodonUsage::Table - for access to the Codon usage Database at http://www.kazusa.or.jp/codon. 5.8.3::Bio::CodonUsage::IO - for reading and writing codon usage tables to file 5.8.3::Bio::Symbol::AlphabetI - A Symbol Alphabet 5.8.3::Bio::Symbol::DNAAlphabet - A ready made DNA alphabet 5.8.3::Bio::Symbol::Symbol - A biological symbol 5.8.3::Bio::Symbol::Alphabet - DESCRIPTION of Object 5.8.3::Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet 5.8.3::Bio::Symbol::SymbolI - Interface for a Symbol 5.8.3::Bio::OntologyIO::InterProParser - Parser for InterPro xml files. 5.8.3::Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format 5.8.3::Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format 5.8.3::Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation type formats 5.8.3::Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats 5.8.3::Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler 5.8.3::Bio::OntologyIO::Handlers::InterProHandler - XML handler class for InterProParser 5.8.3::Bio::OntologyIO::Handlers::BaseSAXHandler - Bio::OntologyIO::Handlers::BaseSAXHandler 5.8.3::Bio::MapIO::mapmaker - A Mapmaker Map reader 5.8.3::Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA Bio::Expression::FeatureI 5.8.3::Bio::Expression::FeatureI - an interface class for DNA/RNA features 5.8.3::Bio::Das::SegmentI - DAS-style access to a feature database 5.8.3::Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types 5.8.3::Bio::ClusterIO::unigene - UniGene input stream 5.8.3::Bio::ClusterIO::dbsnp - dbSNP input stream