Perl modules on tak as of 30 January 2004 generated from pmdesc.pl ======================== AnyDBM_File (1.00) - provide framework for multiple DBMs attributes (0.05) - get/set subroutine or variable attributes AutoLoader (5.59) - load subroutines only on demand AutoSplit (1.0307) - split a package for autoloading autouse (1.03) - postpone load of modules until a function is used base (1.03) - Establish IS-A relationship with base class at compile time Benchmark (1.04) - benchmark running times of Perl code bigint (0.02) - Transparent big integer support for Perl bignum (0.11) - Transparent BigNumber support for Perl bigrat (0.04) - Transparent BigNumber/BigRational support for Perl blib (1.02) - Use MakeMaker's uninstalled version of a package bytes (1.00) - Perl pragma to force byte semantics rather than character semantics Carp (1.01) - warn of errors (from perspective of caller) CGI (2.97) - Simple Common Gateway Interface Class charnames (1.01) - 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 (1.1) - Perl compiler pragma to force verbose warning diagnostics Digest (1.00) - Modules that calculate message digests DirHandle (1.00) - supply object methods for directory handles Dumpvalue (1.11) - provides screen dump of Perl data. English (1.00) - use nice English (or awk) names for ugly punctuation variables Env (1.00) - perl module that imports environment variables as scalars or arrays Exporter (5.566) - Implements default import method for modules Fatal (1.03) - replace functions with equivalents which succeed or die fields (1.02) - compile-time class fields FileCache (1.021) - keep more files open than the system permits FileHandle (2.01) - supply object methods for filehandles filetest (1.00) - Perl pragma to control the filetest permission operators FindBin (1.43) - Locate directory of original perl script if (0.01) - 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 (0.50) - Provide a pseudo-class NEXT that allows method redispatch open (1.01) - perl pragma to set default PerlIO layers for input and output overload (1.00) - Package for overloading perl operations PerlIO (1.01) - On demand loader for PerlIO layers and root of PerlIO::* name space SelectSaver (1.00) - save and restore selected file handle SelfLoader (1.0903) - load functions only on demand Shell (0.4) - run shell commands transparently within perl sort (1.01) - perl pragma to control sort() behaviour sigtrap (1.02) - Perl pragma to enable simple signal handling strict (1.02) - Perl pragma to restrict unsafe constructs subs (1.00) - Perl pragma to predeclare sub names Switch (2.09) - A switch statement for Perl Symbol (1.04) - manipulate Perl symbols and their names Test (1.20) - provides a simple framework for writing test scripts Thread (2.00) - manipulate threads in Perl (for old code only) UNIVERSAL (1.00) - base class for ALL classes (blessed references) utf8 (1.00) - 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 (1.00) - Perl pragma to control VMS-specific language features warnings (1.00) - Perl pragma to control optional warnings Bundle::CPAN (1.58) - A bundle to play with all the other modules on CPAN Attribute::Handlers (0.77) - Simpler definition of attribute handlers Carp::Heavy - no user serviceable parts inside CGI::Apache - Backward compatibility module for CGI.pm CGI::Util (1.3) - Internal utilities used by CGI module CGI::Fast - CGI Interface for Fast CGI CGI::Carp (1.26) - CGI routines for writing to the HTTPD (or other) error log CGI::Push (1.04) - Simple Interface to Server Push CGI::Switch - Backward compatibility module for defunct CGI::Switch CGI::Cookie (1.24) - Interface to Netscape Cookies CGI::Pretty (1.07_00) - module to produce nicely formatted HTML code Class::ISA (0.32) - report the search path for a class's ISA tree Class::Struct (0.61) - declare struct-like datatypes as Perl classes Devel::SelfStubber (1.03) - generate stubs for a SelfLoading module Exporter::Heavy (5.566) - Exporter guts ExtUtils::Constant (0.12) - 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::MakeMaker (6.17) - Create a module Makefile 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 (0.04) - OS adjusted ExtUtils::MakeMaker subclass 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_NW5 (2.06) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_OS2 (1.04) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MY (0.01) - ExtUtils::MakeMaker subclass for customization ExtUtils::MM_VMS (5.70) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_Win95 (0.03) - method to customize MakeMaker for Win9X 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::ParseXS (2.02) - converts Perl XS code into C code ExtUtils::MM_MacOS (1.07) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::Install (1.32) - install files from here to there ExtUtils::MM_Any (0.07) - Platform-agnostic MM methods ExtUtils::MM_Win32 (1.09) - methods to override UN*X behaviour in ExtUtils::MakeMaker ExtUtils::MM_UWIN (0.02) - U/WIN specific subclass of ExtUtils::MM_Unix ExtUtils::Manifest (1.42) - utilities to write and check a MANIFEST file ExtUtils::Command (1.05) - utilities to replace common UNIX commands in Makefiles etc. ExtUtils::MM_Unix (1.42) - methods used by ExtUtils::MakeMaker ExtUtils::Liblist (1.01) - determine libraries to use and how to use them ExtUtils::MakeMaker::bytes (0.01) - Version-agnostic bytes.pm ExtUtils::MakeMaker::vmsish (0.01) - Platform-agnostic vmsish.pm ExtUtils::Command::MM (0.03) - Commands for the MM's to use in Makefiles File::Basename (2.71) - split a pathname into pieces File::CheckTree (4.2) - run many filetest checks on a tree File::Compare (1.1003) - Compare files or filehandles File::Copy (2.05) - Copy files or filehandles File::DosGlob (1.00) - DOS like globbing and then some File::Find (1.04) - Traverse a directory tree. File::Path (1.05) - create or remove directory trees File::Spec (0.86) - 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::Mac (1.4) - File::Spec for Mac OS (Classic) File::Spec::Functions (1.3) - portably perform operations on file names File::Spec::OS2 (1.2) - methods for OS/2 file specs File::Spec::VMS - methods for VMS file specs File::Spec::Unix (1.5) - File::Spec for Unix, base for other File::Spec modules File::Spec::Win32 (1.4) - methods for Win32 file specs File::Spec::Epoc (1.1) - methods for Epoc file specs File::Spec::Cygwin (1.1) - methods for Cygwin file specs Filter::Simple (0.78) - Simplified source filtering Getopt::Long (2.32) - Extended processing of command line options Getopt::Std (1.03) - Process single-character switches with switch clustering Hash::Util (0.04) - A selection of general-utility hash subroutines I18N::Collate (1.00) - compare 8-bit scalar data according to the current locale I18N::LangTags (0.27) - functions for dealing with RFC3066-style language tags I18N::LangTags::List (0.25) - tags and names for human languages IPC::Open2 (1.01) - open a process for both reading and writing IPC::Open3 (1.0104) - open a process for reading, writing, and error handling Math::BigFloat (1.35) - Arbitrary size floating point math package Math::BigInt (1.60) - Arbitrary size integer math package Math::BigRat (0.07) - arbitrarily big rationals Math::Complex (1.34) - complex numbers and associated mathematical functions Math::Trig (1.01) - trigonometric functions Math::BigInt::Calc (0.30) - Pure Perl module to support Math::BigInt Memoize::AnyDBM_File (0.65) - glue to provide EXISTS for AnyDBM_File for Storable use Memoize::Expire (1.00) - Plug-in module for automatic expiration of memoized values Memoize::ExpireFile (1.01) - test for Memoize expiration semantics 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::SMTP (2.26) - Simple Mail Transfer Protocol Client Net::FTP (2.72) - FTP Client class Net::hostent (1.00) - 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 (2.20) - 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 (1.00) - by-name interface to Perl's built-in getserv*() functions Net::Time (2.09) - time and daytime network client interface Net::Domain (2.19) - Attempt to evaluate the current host's internet name and domain PerlIO::via::QuotedPrint (0.04) - PerlIO layer for quoted-printable strings Pod::Checker (1.3) - check pod documents for syntax errors Pod::Find (0.22) - find POD documents in directory trees Pod::Functions (1.01) - Group Perl's functions a la perlfunc.pod Pod::Html (1.04) - module to convert pod files to HTML Pod::InputObjects (1.13) - objects representing POD input paragraphs, commands, etc. Pod::LaTeX (0.54) - Convert Pod data to formatted Latex Pod::Man (1.34) - Convert POD data to formatted *roff input Pod::ParseLink (1.06) - Parse an LEE formatting code in POD text Pod::Parser (1.13) - base class for creating POD filters and translators Pod::ParseUtils (0.22) - helpers for POD parsing and conversion Pod::Plainer (0.01) - Perl extension for converting Pod to old style Pod. Pod::Select (1.13) - extract selected sections of POD from input Pod::Text (2.2) - Convert POD data to formatted ASCII text Pod::Usage (1.14) - print a usage message from embedded pod documentation Pod::Text::Color (1.04) - Convert POD data to formatted color ASCII text Pod::Text::Overstrike (1.09) - Convert POD data to formatted overstrike text Pod::Text::Termcap (1.1) - Convert POD data to ASCII text with format escapes Search::Dict (1.02) - search for key in dictionary file Term::ANSIColor (1.05) - Color screen output using ANSI escape sequences Term::Cap (1.07) - Perl termcap interface Term::Complete (1.4) - Perl word completion module Term::ReadLine (1.00) - Perl interface to various C packages. If no real package is found, substitutes stubs instead of basic functions. Test::Builder (0.15) - Backend for building test libraries Test::More (0.45) - yet another framework for writing test scripts Test::Simple (0.45) - Basic utilities for writing tests. Test::Harness (2.28) - run perl standard test scripts with statistics Test::Harness::Assert (0.01) - simple assert Test::Harness::Iterator (0.01) - Internal Test::Harness Iterator Test::Harness::Straps (0.14) - detailed analysis of test results Text::Abbrev (1.00) - create an abbreviation table from a list Text::Balanced (1.89) - 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 (2001.0929) - line wrapping to form simple paragraphs Thread::Queue (2.00) - thread-safe queues Thread::Semaphore (2.00) - thread-safe semaphores Tie::Array (1.02) - base class for tied arrays Tie::File (0.93) - Access the lines of a disk file via a Perl array Tie::Handle (4.1) - base class definitions for tied handles Tie::Hash (1.00) - base class definitions for tied hashes Tie::Memoize (1.0) - add data to hash when needed Tie::RefHash (1.3) - 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 (1.04) - 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 (0.12) - Unicode Collation Algorithm Unicode::UCD (0.2) - 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 (1.08) - internally used by Encode::JP Encode::KR::2022_KR (1.05) - internally used by Encode::KR Encode::MIME::Header (1.05) - MIME 'B' and 'Q' header encoding Encode::CN::HZ (1.04) - internally used by Encode::CN IO::Socket::INET (1.26) - Object interface for AF_INET domain sockets IO::Socket::UNIX (1.2) - Object interface for AF_UNIX domain sockets List::Util - A selection of general-utility list subroutines Scalar::Util - A selection of general-utility scalar subroutines Graph (0.20101) - graph operations Heap (0.50) - Perl extensions for keeping data partially sorted LWP (5.75) - The World-Wide Web library for Perl URI (1.27) - Uniform Resource Identifiers (absolute and relative) SVG (2.27) - Perl extension for generating Scalable Vector Graphics (SVG) documents GPG (0.05) - a Perl2GnuPG interface Quantum::Superpositions (2.02) - QM-like superpositions in Perl Tie::IxHash (1.21) - ordered associative arrays for Perl GnuPG::Key - GnuPG Key Object GnuPG::Options - GnuPG options embodiment GnuPG::PublicKey - GnuPG Public Key Objects GnuPG::Handles - GnuPG handles bundle GnuPG::UserId - GnuPG User ID Objects GnuPG::Signature - GnuPG Key Signature Objects GnuPG::SubKey - GnuPG Sub Key objects GnuPG::Fingerprint - GnuPG Fingerprint Objects GnuPG::Interface (0.33) - Perl interface to GnuPG GnuPG::SecretKey - GnuPG Secret Key Objects GnuPG::PrimaryKey - GnuPG Primary Key Objects Algorithm::DiffOld (1.1) - Compute `intelligent' differences between two files / lists but use the old (<=0.59) interface. Algorithm::Diff (1.15) - Compute `intelligent' differences between two files / lists GO::OntologyProvider (0.1) - GO::OntologyProvider GO::Reference (0.1) - GO::Reference GO::TermFinder (0.2) - GO::TermFinder GO::AnnotatedGene (0.1) - GO::AnnotatedGene GO::Annotation (0.1) - GO::Annotation GO::AnnotationProvider (0.1) - GO::AnnotationProvider GO::Node (0.1) - GO::Node GO::AnnotationProvider::AnnotationParser (0.1) - GO:AnnotationProvider::AnnotationParser GO::OntologyProvider::OntologyParser (0.1) - GO::OntologyProvider::OntologyParser CGI::Session (3.95) - persistent session data in CGI applications CGI::Session::DB_File (0.1) - DB_File driver for CGI::Session CGI::Session::BluePrint (0.1) - Default CGI::Session driver BluePrint CGI::Session::MySQL (3.2.4.2) - MySQL driver for CGI::Session CGI::Session::CookBook (3.1.4.1) - tutorial on session management in cgi applications CGI::Session::Example - Example on using CGI::Session CGI::Session::Tutorial - extended CGI::Session manual CGI::Session::PostgreSQL (1.2) - PostgreSQL driver for CGI::Session CGI::Session::File (3.1.4.1) - Default CGI::Session driver CGI::Session::ID::MD5 (3.2) - default CGI::Session ID driver CGI::Session::ID::SHA1 - SHA1 session id generator CGI::Session::ID::Incr (3.1) - CGI::Session ID driver CGI::Session::Serialize::Default (1.5) - default serializer for CGI::Session CGI::Session::Serialize::Storable (1.4) - serializer for CGI::Session CGI::Session::Serialize::FreezeThaw (1.3) - serializer for CGI::Session Authen::SASL::Perl::DIGEST_MD5 (1.00) - SWF::BinStream (0.071) - SWF::Element (0.24) - SWF::Parser (0.051) - SWF::File (0.031) - SWF::BinStream::File (0.041) - SWF::BinStream::Codec::Zlib (0.01) - SWF::BinStream codec to add zlib-compression/decompression. SVG::DOM (1.01) - A library of DOM (Document Object Model) methods for SVG objects. SVG::XML (2.26) - Handle the XML generation bits for SVG.pm SVG::Manual - Perl extension for generating Scalable Vector Graphics (SVG) documents SVG::Element (2.26) - Generate the element bits for SVG.pm Archive::Tar (1.07) - module for manipulations of tar archives Archive::Tar::File - a subclass for in-memory extracted file from Archive::Tar Email::Valid (0.14) - Check validity of Internet email addresses Mail::Cap (1.58) - Parse mailcap files Mail::Util (1.58) - mail utility functions Mail::Address (1.58) - Parse mail addresses Mail::Mailer (1.58) - Simple interface to electronic mailing mechanisms Mail::Send (1.58) - Simple electronic mail interface Mail::Header (1.58) - manipulate mail RFC822 compliant headers Mail::Internet (1.58) - manipulate Internet format (RFC 822) mail messages Mail::Filter (1.58) - Filter mail through multiple subroutines Mail::Field (1.58) - Base class for manipulation of mail header fields Mail::Field::AddrList (1.58) - object representation of e-mail address lists Attribute::Handlers (0.77) - Simpler definition of attribute handlers Getopt::Auto - Framework for command-line applications URI::data - URI that contain immediate data URI::QueryParam - Additional query methods for URIs URI::ldap (1.10) - LDAP Uniform Resource Locators URI::URL (5.03) - Uniform Resource Locators URI::file (4.13) - URI that map to local file names URI::WithBase (2.19) - URIs which remember their base URI::Heuristic (4.16) - Expand URI using heuristics URI::Escape (3.21) - Escape and unescape unsafe characters URI::Split - Parse and compose URI strings B::Utils (0.04_01) - Helper functions for op tree manipulation Module::Info (0.20) - Information about Perl modules Module::Build (0.18) - Build and install Perl modules Module::Build::Base - Default methods for Module::Build Module::Build::Compat (0.02) - Compatibility with ExtUtils::MakeMaker Module::Build::Platform::MPEiX - Builder class for MPEiX platforms Module::Build::Platform::EBCDIC - Builder class for EBCDIC platforms Module::Build::Platform::VMS - Builder class for VMS platforms Module::Build::Platform::VOS - Builder class for VOS platforms Module::Build::Platform::darwin - Builder class for Mac OS X platform Module::Build::Platform::Default - Stub class for unknown platforms Module::Build::Platform::RiscOS - Builder class for RiscOS platforms Module::Build::Platform::Amiga - Builder class for Amiga platforms Module::Build::Platform::Windows - Builder class for Windows platforms Module::Build::Platform::MacOS - Builder class for MacOS platforms Module::Build::Platform::Unix - Builder class for Unix platforms YAML::Node - A generic data node that encapsulates YAML information Log::Log4perl (0.35) - Log4j implementation for Perl Log::Dispatch (2.06) - Dispatches messages to multiple Log::Dispatch::* objects Log::Dispatch::Base (1.09) - Code shared by dispatch and output objects. Log::Dispatch::Handle (1.16) - Object for logging to IO::Handle objects (and subclasses thereof) Log::Dispatch::Output (1.26) - Base class for all Log::Dispatch::* object Log::Dispatch::Screen (1.17) - Object for logging to the screen Log::Dispatch::File (1.22) - Object for logging to files Log::Dispatch::ApacheLog - Object for logging to Apache::Log objects Log::Dispatch::Email (1.19) - Base class for objects that send log messages via email Log::Dispatch::Syslog (1.18) - Object for logging to system log. Log::Dispatch::FileRotate (1.09) - Log to files that archive/rotate themselves Log::Dispatch::Email::MIMELite (1.19) - Subclass of Log::Dispatch::Email that uses the MIME::Lite module Log::Dispatch::Email::MailSendmail - Subclass of Log::Dispatch::Email that uses the Mail::Sendmail module Log::Dispatch::Email::MailSender - Subclass of Log::Dispatch::Email that uses the Mail::Sender module Log::Dispatch::Email::MailSend (1.19) - Subclass of Log::Dispatch::Email that uses the Mail::Send module Log::Log4perl::FAQ - Frequently Asked Questions on Log::Log4perl Log::Log4perl::MDC - Mapped Diagnostic Context Log::Log4perl::NDC - Nested Diagnostic Context Log::Log4perl::Level - Predefined log levels Log::Log4perl::Layout (-1, set by base.pm) - Log4perl Layout Virtual Base Class Log::Log4perl::Appender - Log appender class Log::Log4perl::DateFormat - Log4perl advanced date formatter helper class Log::Log4perl::Config - Log4perl configuration file syntax Log::Log4perl::Filter - Log4perl Custom Filter Base Class Log::Log4perl::JavaMap - maps java log4j appenders to Log::Dispatch classes Log::Log4perl::Logger - Main Logger Class Log::Log4perl::Config::PropertyConfigurator - reads properties file Log::Log4perl::Config::Watch - Detect file changes Log::Log4perl::Config::DOMConfigurator (0.03) - reads xml config files Log::Log4perl::Filter::LevelMatch - Filter to match the log level exactly Log::Log4perl::Filter::LevelRange - Filter for a range of log levels Log::Log4perl::Filter::Boolean - Special filter to combine the results of others Log::Log4perl::Filter::StringMatch - Filter to match the log level exactly Log::Log4perl::Layout::NoopLayout - Pass-thru Layout Log::Log4perl::Layout::PatternLayout - Pattern Layout Log::Log4perl::Layout::SimpleLayout - Simple Layout Log::Log4perl::Appender::TestArrayBuffer - Subclass of Appender::TestBuffer Log::Log4perl::Appender::Screen - Log to STDOUT/STDERR Log::Log4perl::Appender::TestBuffer - Appender class for testing Log::Log4perl::Appender::File - Log to file Log::Log4perl::Appender::DBI - implements appending to a DB Log::Log4perl::JavaMap::RollingFileAppender - wraps Log::Dispatch::FileRotate Log::Log4perl::JavaMap::ConsoleAppender - wraps Log::Dispatch::Screen Log::Log4perl::JavaMap::JDBCAppender - wraps Log::Log4perl::Appender::DBI Log::Log4perl::JavaMap::TestBuffer - wraps Log::Log4perl::Appender::TestBuffer Log::Log4perl::JavaMap::FileAppender - wraps Log::Dispatch::File Log::Log4perl::JavaMap::SyslogAppender - wraps Log::Dispatch::Syslog Log::Log4perl::JavaMap::NTEventLogAppender - wraps Log::Dispatch::Win32EventLog DB_File::Lock (0.05) - Locking with flock wrapper for DB_File LWP::MediaTypes (1.30) - guess media type for a file or a URL LWP::ConnCache (0.01) - Connection cache manager LWP::RobotUA (1.23) - a class for well-behaved Web robots LWP::Simple (1.38) - simple procedural interface to LWP LWP::Protocol (1.41) - Base class for LWP protocols LWP::UserAgent (2.023) - Web user agent class LWP::MemberMixin - Member access mixin class LWP::DebugFile - routines for tracing/debugging LWP LWP::Debug - debug routines for the libwww-perl library LWP::Authen::Ntlm - Library for enabling NTLM authentication (Microsoft) in LWP Net::HTTP (1.00) - Low-level HTTP connection (client) Net::AIM (1.22) - Perl extension for AOL Instant Messenger TOC protocol Net::LDAPI (0.02) - use LDAP over a UNIX domain socket Net::LDAPS (0.05) - use LDAP over an SSL connection Net::Telnet (3.03) - interact with TELNET port or other TCP ports Net::LDAP::Util (0.10) - Utility functions Net::LDAP::DSML (0.12) - A DSML Writer for Net::LDAP Net::LDAP::RootDSE (0.01) - An LDAP RootDSE object Net::LDAP::Control (0.04) - LDAPv3 control object base class Net::LDAP::Constant (0.02) - Constants for use with Net::LDAP Net::LDAP::Extra (0.01) - Load extra Net::LDAP methods Net::LDAP::Control::VLVResponse (0.03) - LDAPv3 Virtual List View server response Net::LDAP::Control::VLV (0.03) - LDAPv3 Virtual List View control object Net::LDAP::Control::SortResult - Server Side Sort (SSS) result control object Net::LDAP::Control::ProxyAuth (1.03) - LDAPv3 Proxy Authentication control object Net::LDAP::Control::Sort (0.02) - Server Side Sort (SSS) control object Net::LDAP::Control::Paged (0.02) - LDAPv3 Paged results control object Net::AIM::Event - Object to hold event data Net::AIM::Connection - Interface to an AIM connection Net::HTTP::NB (0.02) - Non-blocking HTTP client WWW::SMS (0.09) - sends SMS using service provided by free websites WWW::RobotRules (1.26) - database of robots.txt-derived permissions WWW::RobotRules::AnyDBM_File (1.11) - Persistent RobotRules HTML::Tagset (3.03) - data tables useful in parsing HTML HTML::Form (1.038) - Class that represents an HTML form element HTTP::Date (1.46) - date conversion routines HTTP::Request (1.34) - HTTP style request message HTTP::Cookies (1.36) - HTTP cookie jars 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::Daemon (1.33) - a simple http server class HTTP::Message (1.30) - HTTP style message base class HTTP::Status (1.28) - HTTP Status code processing HTTP::Cookies::Microsoft - access to Microsoft cookies files HTTP::Cookies::Netscape (1.26) - access to Netscape cookies files HTTP::Request::Common (1.22) - Construct common HTTP::Request objects HTTP::Headers::Util (1.13) - Header value parsing utility functions File::Listing (1.15) - parse directory listing Bundle::LWP (1.10) - install all libwww-perl related modules Bundle::Net::LDAP (0.02) - A bundle for Net::LDAP Class::MethodMaker (1.12) - a module for creating generic methods Bio::SeqFeatureI - Abstract interface of a Sequence Feature Bio::Biblio (1.7) - A Bibliographic Query Service module Bio::IdCollectionI - interface for objects with multiple identifiers Bio::MapIO - A Map Factory object Bio::LocationI - Abstract interface of a Location on a Sequence Bio::ClusterI - Cluster Interface Bio::RangeI - Range interface Bio::TreeIO - Parser for Tree files Bio::Perl - Functional access to BioPerl for people who don't know objects Bio::ClusterIO - Handler for Cluster Formats Bio::AnalysisParserI - Generic analysis output parser interface Bio::Range - Pure perl RangeI implementation Bio::AnnotationCollectionI - Interface for annotation collections Bio::Species - Generic species object Bio::Taxonomy - Conversion used bt the Taxonomy classes Bio::Seq (1.1) - Sequence object, with features Bio::AlignIO - Handler for AlignIO Formats Bio::AnnotationI - Annotation interface Bio::DasI - DAS-style access to a feature database Bio::SeqAnalysisParserI - Sequence analysis output parser interface Bio::SeqI - Abstract Interface of Sequence (with features) 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. Bio::SearchIO - Driver for parsing Sequence Database Searches (Blast,FASTA,...) Bio::SimpleAlign - Multiple alignments held as a set of sequences Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references Bio::OntologyIO - Parser factory for Ontology formats Bio::SeqUtils - Additional methods for PrimarySeq objects Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq Bio::DescribableI - interface for objects with human readable names and descriptions Bio::FeatureHolderI - the base interface an object with features must implement Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates Bio::SearchDist (Can't locate Bio/Ext/Align.pm in @INC (@INC contains: /cluster/lsfpool/perl/lib/perl5/5.8.0 /cluster/lsfpool/perl/lib/perl5/site_perl /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0 /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld/auto /cluster/lsfpool/perl/lib/perl5/5.8.0/i686-linux-thread-multi-ld/auto /cluster/lsfpool/RSPerl/share/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/5.8.0 /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0 /cluster/lsfpool/perl/lib/perl5/site_perl /cluster/lsfpool/perl/lib/perl5/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/5.8.0 /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0 /cluster/lsfpool/perl/lib/perl5/site_perl /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0 /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld/auto /cluster/lsfpool/perl/lib/perl5/5.8.0/i686-linux-thread-multi-ld/auto /cluster/lsfpool/RSPerl/share/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/i686-linux-thread-multi-ld .) at /cluster/lsfpool/perl/lib/perl5/site_perl/5.8.0/Bio/SearchDist.pm line 109.) - A perl wrapper around Sean Eddy's histogram object Bio::IdentifiableI - interface for objects with identifiers Bio::AnalysisResultI - Interface for analysis result objects Bio::AnnotatableI - the base interface an annotatable object must implement Bio::PrimarySeq - Bioperl lightweight Sequence Object Bio::UnivAln (1.01) - Bioperl alignment object Bio::MAGE (20020902.6) - Container module for classes in the MAGE MAGE package Bio::AnalysisI - An interface to any (local or remote) analysis tool Bio::SeqIO - Handler for SeqIO Formats Bio::Graphics (1.2003) - Generate GD images of Bio::Seq objects Bio::MAGE::HigherLevelAnalysis (20020902.6) - Container module for classes in the MAGE HigherLevelAnalysis package Bio::MAGE::DesignElement (20020902.6) - Container module for classes in the MAGE DesignElement package Bio::MAGE::SQLUtils - a module for exporting MAGE-OM objects to a database Bio::MAGE::QuantitationType (20020902.6) - Container module for classes in the MAGE QuantitationType package Bio::MAGE::BioAssayData (20020902.6) - Container module for classes in the MAGE BioAssayData package Bio::MAGE::BioMaterial (20020902.6) - Container module for classes in the MAGE BioMaterial package Bio::MAGE::Protocol (20020902.6) - Container module for classes in the MAGE Protocol package Bio::MAGE::Array (20020902.6) - Container module for classes in the MAGE Array package Bio::MAGE::AuditAndSecurity (20020902.6) - Container module for classes in the MAGE AuditAndSecurity package Bio::MAGE::BioEvent (20020902.6) - Container module for classes in the MAGE BioEvent package Bio::MAGE::Description (20020902.6) - Container module for classes in the MAGE Description package Bio::MAGE::ArrayDesign (20020902.6) - Container module for classes in the MAGE ArrayDesign package Bio::MAGE::Measurement (20020902.6) - Container module for classes in the MAGE Measurement package Bio::MAGE::BioSequence (20020902.6) - Container module for classes in the MAGE BioSequence package Bio::MAGE::Experiment (20020902.6) - Container module for classes in the MAGE Experiment package Bio::MAGE::BQS (20020902.6) - Container module for classes in the MAGE BQS package Bio::MAGE::BioAssay (20020902.6) - Container modieving sequences Bio::DB::GDB - Database object interface to GDB HTTP query Bio::DB::GFF (1.2003) - Storage and retrieval of sequence annotation data Bio::DB::RefSeq - Database object interface for RefSeq retrieval Bio::DB::EMBL - Database object interface for EMBL entry retrieval Bio::DB::XEMBL - Database object interface for XEMBL entry retrieval Bio::DB::XEMBLService - SOAP service definition for XEMBL Bio::DB::BiblioI (1.5) - An interface to a Bibliographic Query Service Bio::DB::GenPept - Database object interface to GenPept Bio::DB::QueryI (0.1) - Object Interface to queryable sequence databases Bio::DB::NCBIHelper (0.8) - A collection of routines useful for queries to NCBI databases. Bio::DB::SeqI - Abstract Interface for Sequence databases Bio::DB::FileCache - In file cache for BioSeq objects Bio::DB::Universal - Artificial database that delegates to specific databases Bio::DB::RandomAccessI - Abstract interface for a sequence database Bio::DB::DBFetch - Database object for retrieving using the dbfetch script Bio::DB::SwissProt - Database object interface to SwissProt retrieval Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences. Bio::DB::Flat - Interface for indexed flat files Bio::DB::InMemoryCache - Abstract interface for a sequence database Bio::DB::Ace - Database object interface to ACeDB servers Bio::DB::Registry (1.2) - Access to the Open Bio Database Access registry scheme Bio::DB::GenBank - Database object interface to GenBank Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs Bio::DB::BioFetch (1.0) - Database object interface to BioFetch retrieval Bio::DB::Das::Chado (0.11) - DAS-style access to a chado database Bio::DB::Das::BioSQL - DAS-style access to a BioSQL database Bio::DB::Das::BioSQL::Segment (0.01) - DAS-style access to a BioSQL database Bio::DB::Das::Chado::Segment (0.11) - DAS-style access to a chado database Bio::DB::Das::Chado::Segment::Feature (0.11) - Bio::DB::GFF::Aggregator - Aggregate GFF groups into composite features Bio::DB::GFF::Homol - A segment of DNA that is homologous to another Bio::DB::GFF::RelSegment - Sequence segment with relative coordinate support Bio::DB::GFF::Typename - The name of a feature type Bio::DB::GFF::Featname - The name of a feature Bio::DB::GFF::Segment - Simple DNA segment object Bio::DB::GFF::Feature - A relative segment identified by a feature type Bio::DB::GFF::Util::Rearrange - rearrange utility Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index Bio::DB::GFF::Aggregator::ucsc_acembly - UCSC acembly aggregator Bio::DB::GFF::Aggregator::clone - Clone aggregator Bio::DB::GFF::Aggregator::ucsc_sanger22 - UCSC sanger22 aggregator Bio::DB::GFF::Aggregator::ucsc_refgene - UCSC refGene aggregator Bio::DB::GFF::Aggregator::match - Match aggregator Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo - UCSC sanger22pseudo aggregator Bio::DB::GFF::Aggregator::ucsc_twinscan - UCSC twinscan aggregator Bio::DB::GFF::Aggregator::transcript - Transcript aggregator Bio::DB::GFF::Aggregator::coding - The Coding Region Aggregator Bio::DB::GFF::Aggregator::alignment - Alignment aggregator Bio::DB::GFF::Aggregator::ucsc_unigene - UCSC UniGene aggregator Bio::DB::GFF::Aggregator::ucsc_ensgene - UCSC ensGene aggregator Bio::DB::GFF::Aggregator::ucsc_genscan - UCSC genscan aggregator Bio::DB::GFF::Aggregator::wormbase_gene (0.30) - Wormbase gene aggregator Bio::DB::GFF::Aggregator::reftranscript (0.10) - Aggregates references transcripts Bio::DB::GFF::Aggregator::waba_alignment (0.20) - A WABA alignment Bio::DB::GFF::Aggregator::orf (1.00) - An aggregator for orf regions Bio::DB::GFF::Aggregator::ucsc_softberry - UCSC softberry aggregator Bio::DB::GFF::Aggregator::none - No aggregation Bio::DB::GFF::Aggregator::processed_transcript - Sequence Ontology Transcript Bio::DB::GFF::Adaptor::biofetch - Cache BioFetch objects in a Bio::DB::GFF database Bio::DB::GFF::Adaptor::ace - ace interface (for multiple inheritance) Bio::DB::GFF::Adaptor::dbi - Database adaptor for DBI (SQL) databases Bio::DB::GFF::Adaptor::memory - Database adaptor for a specific mysql schema Bio::DB::GFF::Adaptor::memory_iterator - iterator for Bio::DB::GFF::Adaptor::memory Bio::DB::GFF::Adaptor::dbi::oracleace - Unholy union between oracle GFF database and acedb database Bio::DB::GFF::Adaptor::dbi::mysqlace - Unholy union between mysql GFF database and acedb database Bio::DB::GFF::Adaptor::dbi::iterator - iterator for Bio::DB::GFF::Adaptor::dbi 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::oracle - Database adaptor for a specific oracle schema Bio::DB::GFF::Adaptor::dbi::caching_handle - Cache for database handles Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file Bio::DB::Flat::OBDAIndex - Binary search indexing system for sequence files Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file Bio::DB::Biblio::soap (1.5) - A SOAP-based access to a bibliographic query service Bio::DB::Biblio::biofetch (1.5) - A BioFetch-based access to a bibliographic citation retrieval Bio::DB::Query::WebQuery (0.1) - Helper class for web-based sequence queryies Bio::DB::Query::GenBank (0.2) - Build a GenBank Entrez Query Bio::Das::SegmentI (1) - DAS-style access to a feature database Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types Bio::Map::MarkerI - Interface for basic marker functionality 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. Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap Bio::Map::LinkageMap - A representation of a genetic linkage map. Bio::Map::Position - A single position of a Marker in a Map Bio::Map::Microsatellite - An object representing a Microsatellite marker. Bio::Map::MappableI - An object that can be placed in a map 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. Bio::Map::CytoMarker - An object representing a marker. Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map Bio::Map::CytoPosition (1) - Marker class with cytogenetic band storing attributes Bio::Map::MapI - Interface for describing Map objects in bioperl Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps. Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor 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 Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace Bio::Seq::EncodedSeq - subtype of L to store DNA that encodes a protein Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object Bio::Seq::SeqFastaSpeedFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality Bio::Root::Err (0.041) - Exception class for Perl 5 objects Bio::Root::IO - module providing several methods often needed when dealing with file IO Bio::Root::Exception - Generic exception objects for Bioperl Bio::Root::RootI (1) - Abstract interface to root object code Bio::Root::HTTPget - module for fallback HTTP get operations when LWP:: is unavailable Bio::Root::Object (0.041) - A core Perl 5 object. Bio::Root::Vector (0.04) - Interface for managing linked lists of Perl5 objects. Bio::Root::Global - Global variables and utility functions Bio::Root::Xref (0.01) - A generic cross-reference object. Bio::Root::Root (1) - Hash-based implementation of Bio::Root::RootI Bio::Root::Utilities (0.05) - General-purpose utility module Bio::Root::IOManager (0.043) - Input and output manager for Perl5 objects. Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags Bio::Tree::NodeI - Interface describing a Tree Node Bio::Tree::Statistics - Calculate certain statistics for a Tree Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. Bio::Tree::Tree - An Implementation of TreeI interface. Bio::Tree::Node - A Simple Tree Node Bio::Tree::RandomFactory - TreeFactory for generating Random Trees Bio::Tree::AlleleNode - DESCRIPTION of Object Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods Bio::Biblio::IO - Handling the bibliographic references Bio::Biblio::Person - Representation of a person Bio::Biblio::Journal - Representation of a journal Bio::Biblio::BookArticle - Representation of a book article Bio::Biblio::MedlineJournalArticle - Representation of a MEDLINE journal article Bio::Biblio::Ref - Representation of a bibliographic reference Bio::Biblio::Book - Representation of a book Bio::Biblio::Thesis - Representation of thesis Bio::Biblio::PubmedBookArticle - Representation of a PUBMED book article Bio::Biblio::Organisation - Representation of an organisation Bio::Biblio::MedlineBook - Representation of a MEDLINE book Bio::Biblio::Service - Representation of a provider of type service Bio::Biblio::MedlineArticle - Representation of a MEDLINE article Bio::Biblio::MedlineBookArticle - Representation of a MEDLINE book article Bio::Biblio::PubmedJournalArticle - Representation of a PUBMED journal article Bio::Biblio::BiblioBase - An abstract base for other biblio classes Bio::Biblio::Proceeding - Representation of a conference proceeding Bio::Biblio::Article - Representation of a general article Bio::Biblio::Provider - Representation of a general provider Bio::Biblio::JournalArticle - Representation of a journal article Bio::Biblio::WebResource - Representation of a web resource Bio::Biblio::Patent - Representation of a patent Bio::Biblio::PubmedArticle - Representation of a PUBMED article Bio::Biblio::TechReport - Representation of a technical report Bio::Biblio::MedlineJournal - Representation of a MEDLINE journal Bio::Biblio::IO::medline2ref (1.10) - 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 (1.2) - A converter of a raw hash to PUBMED citations Bio::Biblio::IO::medlinexml (1.5) - A converter of XML files with MEDLINE citations Bio::Expression::FeatureI - an interface class for DNA/RNA features Bio::Expression::FeatureSet - a set of DNA/RNA features. ISA Bio::Expression::FeatureI Bio::Expression::ProbeI - an interface class for DNA/RNA probes Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA Bio::Expression::FeatureI Bio::AlignIO::phylip - PHYLIP format sequence input/output stream Bio::AlignIO::fasta - FastA MSA Sequence input/output stream Bio::AlignIO::mase - mase sequence input/output stream Bio::AlignIO::mega - Parse and Create MEGA format data files Bio::AlignIO::meme - meme sequence input/output stream Bio::AlignIO::clustalw - clustalw sequence input/output stream Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle) Bio::AlignIO::msf - msf sequence input/output stream Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files Bio::AlignIO::selex - selex sequence input/output stream Bio::AlignIO::prodom - prodom sequence input/output stream Bio::AlignIO::pfam - pfam sequence input/output stream Bio::AlignIO::stockholm - stockholm sequence input/output stream Bio::AlignIO::bl2seq - bl2seq sequence input/output stream Bio::AlignIO::nexus - NEXUS format sequence input/output stream Bio::Align::AlignI - An interface for describing sequence alignments. Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment Bio::Align::StatisticsI - Calculate some statistics for an alignment Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects Bio::Event::EventHandlerI - An Event Handler Interface Bio::Event::EventGeneratorI - This interface describes the basic event generator class. Bio::Index::Fasta (0.2) - Interface for indexing (multiple) fasta files Bio::Index::Fastq (0.2) - Interface for indexing (multiple) fastq files Bio::Index::EMBL (0.1) - Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). Bio::Index::Abstract - Abstract interface for indexing a flat file Bio::Index::GenBank (0.1) - Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). Bio::Index::AbstractSeq - Base class for AbstractSeq s Bio::Index::Swissprot (0.1) - Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). Bio::Index::SwissPfam (0.1) - Interface for indexing swisspfam files Bio::Index::Blast (0.1) - Indexes Blast reports and supports retrieval based on query accession(s) Bio::MapIO::mapmaker - A Mapmaker Map reader Bio::SeqIO::embl - EMBL sequence input/output stream Bio::SeqIO::qual - .qual file input/output stream Bio::SeqIO::chadosxpr - chadosxpr sequence input/output stream Bio::SeqIO::chado - chado sequence input/output stream Bio::SeqIO::fasta - fasta sequence input/output stream Bio::SeqIO::game - Parses GAME XML 0.1 and higher into and out of Bio::Seq objects. Bio::SeqIO::fastq - fastq sequence input/output stream Bio::SeqIO::abi - abi trace sequence input/output stream Bio::SeqIO::ace - ace sequence input/output stream Bio::SeqIO::largefasta - method i/o on very large fasta sequence files Bio::SeqIO::alf - alf trace sequence input/output stream Bio::SeqIO::chadoxml - chadoxml sequence input/output stream Bio::SeqIO::ctf - ctf trace sequence input/output stream Bio::SeqIO::exp - exp trace sequence input/output stream Bio::SeqIO::gcg - GCG sequence input/output stream Bio::SeqIO::phd - .phd file input/output stream Bio::SeqIO::pir - PIR sequence input/output stream Bio::SeqIO::pln - pln trace sequence input/output stream Bio::SeqIO::raw - raw sequence file input/output stream Bio::SeqIO::scf - .scf file input/output stream Bio::SeqIO::ztr - ztr trace sequence input/output stream Bio::SeqIO::MultiFile - Treating a set of files as a single input stream Bio::SeqIO::locuslink - DESCRIPTION of Object Bio::SeqIO::chadoitext - chadoitext sequence input/output stream Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables Bio::SeqIO::bsml - BSML sequence input/output stream Bio::SeqIO::genbank - GenBank sequence input/output stream Bio::SeqIO::swiss - Swissprot sequence input/output stream Bio::SeqIO::game::seqHandler - GAME helper via PerlSAX helper. Bio::SeqIO::game::idHandler - GAME helper via PerlSAX helper. Bio::SeqIO::game::featureHandler - GAME helper via PerlSAX helper. Bio::Tools::Profile - parse Profile output Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser Bio::Tools::Pseudowise - Results of one Pseudowise run Bio::Tools::Tmhmm - parse TmHMM output (transmembrane HMM) Bio::Tools::Genomewise - Results of one Genomewise run Bio::Tools::Gel - Calculates relative electrophoretic migration distances Bio::Tools::AlignFactory - Base object for alignment factories Bio::Tools::EPCR - Parse ePCR output and make features Bio::Tools::Hmmpfam - Bio::Tools::Hmmpfam Bio::Tools::Eponine - Results of one Eponine run Bio::Tools::Seg - parse Seg output (filter low complexity protein sequence) Bio::Tools::SeqAnal (0.011) - Bioperl sequence analysis base class. Bio::Tools::SeqWords - Object holding n-mer statistics for one sequence Bio::Tools::ECnumber - representation of EC numbers Bio::Tools::WWW (0.014) - Bioperl manager for web resources related to biology. Bio::Tools::Genewise - Results of one Genewise run Bio::Tools::ESTScan - Results of one ESTScan run Bio::Tools::Coil - Bio::Tools::Coil Bio::Tools::SeqStats - Object holding statistics for one particular sequence Bio::Tools::Primer3 - Create input for and work with the output from the program primer3 Bio::Tools::Sigcleave (0.02) - Bioperl object for sigcleave analysis Bio::Tools::Genscan - Results of one Genscan run Bio::Tools::BPlite - Lightweight BLAST parser Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects Bio::Tools::MZEF - Results of one MZEF run Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object Bio::Tools::BPpsilite - Lightweight BLAST parser for (iterated) psiblast reports Bio::Tools::pSW - pairwise Smith Waterman object Bio::Tools::Prints - Parser for FingerPRINTScanII program Bio::Tools::FootPrinter - DESCRIPTION of Object Bio::Tools::BPbl2seq - Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm. Bio::Tools::Lucy (0.01) - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR Bio::Tools::Grail - Results of one Grail run Bio::Tools::Signalp - Bio::Tools::SignalP Bio::Tools::CodonTable - Bioperl codon table object Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers Bio::Tools::RestrictionEnzyme - Bioperl object for a restriction endonuclease (cuts DNA at specific locations) Bio::Tools::RepeatMasker - DESCRIPTION of Object Bio::Tools::Blast (0.09) - Bioperl BLAST sequence analysis object Bio::Tools::SeqPattern (0.011) - Bioperl object for a sequence pattern or motif Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence Bio::Tools::Genemark - Results of one Genemark run Bio::Tools::Promoterwise - DESCRIPTION of Object Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP Bio::Tools::Run::StandAloneBlast - Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq) Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications Bio::Tools::Run::PiseApplication - A class manage Pise programs information, configuring parameters and submit jobs. Bio::Tools::Run::Profile - Bio::Tools::Run::Profile Bio::Tools::Run::Pseudowise - Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes in a given protein seequence. Bio::Tools::Run::Hmmpfam - Bio::Tools::Run::Hmmpfam Bio::Tools::Run::Eponine - Object for execution of the Eponine which is a mammalian TSS predictor Bio::Tools::Run::Seg - Object for identifying low complexity regions in a given protein seequence. Bio::Tools::Run::Genewise - Object for predicting genes in a given sequence given a protein Bio::Tools::Run::Analysis - Module representing any (remote or local) analysis tool Bio::Tools::Run::TribeMCL - Bio::Tools::Run::TribeMCL Bio::Tools::Run::Primate - Wrapper for Primate, Guy Slater's near exact match finder for short sequence tags. Bio::Tools::Run::Coil - Bio::Tools::Run::Coil Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a matrix(for appropriate organisms). Bio::Tools::Run::Prints - Bio::Tools::Run::Prints Bio::Tools::Run::Mdust (0.01) - Perl extension for Mdust nucleotide filtering Bio::Tools::Run::FootPrinter - Wrapper for FootPrinter Program Bio::Tools::Run::PiseJobParser - A class to parse a Pise server XHTML output. Bio::Tools::Run::PiseJob (1.0) - A class to manage Pise jobs. Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using promoterwise Bio::Tools::Run::Vista - Bio::Tools::Run::Vista Bio::Tools::Run::Signalp - Bio::Tools::Run::Signalp Bio::Tools::Run::AnalysisFactory - A directory of analysis tools Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program codeml Bio::Tools::Run::Phylo::Molphy::ProtML - A wrapper for the Molphy pkg app ProtML Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules Bio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip program protdist Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip program SeqBoot Bio::Tools::Run::Phylo::Phylip::Neighbor - Wrapper for the phylip program neighbor by Joseph Felsenstein for creating a phylogenetic tree(either through Neighbor or UPGMA) based on protein distances based on amino substitution rate. Bio::Tools::Run::Phylo::Phylip::PhylipConf - Bio::Tools::Run::Phylo::Phylip::PhylipConf Bio::Tools::Run::Phylo::Phylip::Consense - Wrapper for the phylip program Consense Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree program to draw trees Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a L object from a multiple alignment file or a SimpleAlign object Bio::Tools::Run::Phylo::Phylip::DrawGram - use Phylip DrawTree program to draw phylograms or phenograms Bio::Tools::Run::PiseApplication::infoseq - Bio::Tools::Run::PiseApplication::infoseq Bio::Tools::Run::PiseApplication::combat - Bio::Tools::Run::PiseApplication::combat Bio::Tools::Run::PiseApplication::pyreval - Bio::Tools::Run::PiseApplication::pyreval Bio::Tools::Run::PiseApplication::bionj - Bio::Tools::Run::PiseApplication::bionj Bio::Tools::Run::PiseApplication::Puzzle - Bio::Tools::Run::PiseApplication::Puzzle Bio::Tools::Run::PiseApplication::distquart - Bio::Tools::Run::PiseApplication::distquart Bio::Tools::Run::PiseApplication::consense - Bio::Tools::Run::PiseApplication::consense Bio::Tools::Run::PiseApplication::lgicsearch - Bio::Tools::Run::PiseApplication::lgicsearch Bio::Tools::Run::PiseApplication::antigenic - Bio::Tools::Run::PiseApplication::antigenic Bio::Tools::Run::PiseApplication::backtranseq - Bio::Tools::Run::PiseApplication::backtranseq Bio::Tools::Run::PiseApplication::cons - Bio::Tools::Run::PiseApplication::cons Bio::Tools::Run::PiseApplication::patmatmotifs - Bio::Tools::Run::PiseApplication::patmatmotifs Bio::Tools::Run::PiseApplication::remap - Bio::Tools::Run::PiseApplication::remap Bio::Tools::Run::PiseApplication::whichdb - Bio::Tools::Run::PiseApplication::whichdb Bio::Tools::Run::PiseApplication::transeq - Bio::Tools::Run::PiseApplication::transeq Bio::Tools::Run::PiseApplication::dnadist - Bio::Tools::Run::PiseApplication::dnadist Bio::Tools::Run::PiseApplication::splitter - Bio::Tools::Run::PiseApplication::splitter Bio::Tools::Run::PiseApplication::njdist - Bio::Tools::Run::PiseApplication::njdist Bio::Tools::Run::PiseApplication::melting - Bio::Tools::Run::PiseApplication::melting Bio::Tools::Run::PiseApplication::dialign2 - Bio::Tools::Run::PiseApplication::dialign2 Bio::Tools::Run::PiseApplication::hmoment - Bio::Tools::Run::PiseApplication::hmoment Bio::Tools::Run::PiseApplication::addquart - Bio::Tools::Run::PiseApplication::addquart Bio::Tools::Run::PiseApplication::stride - Bio::Tools::Run::PiseApplication::stride Bio::Tools::Run::PiseApplication::degapseq - Bio::Tools::Run::PiseApplication::degapseq Bio::Tools::Run::PiseApplication::scopparse - Bio::Tools::Run::PiseApplication::scopparse Bio::Tools::Run::PiseApplication::cusp - Bio::Tools::Run::PiseApplication::cusp Bio::Tools::Run::PiseApplication::fuzztran - Bio::Tools::Run::PiseApplication::fuzztran Bio::Tools::Run::PiseApplication::pepnet - Bio::Tools::Run::PiseApplication::pepnet Bio::Tools::Run::PiseApplication::makehist - Bio::Tools::Run::PiseApplication::makehist Bio::Tools::Run::PiseApplication::rnaheat - Bio::Tools::Run::PiseApplication::rnaheat Bio::Tools::Run::PiseApplication::xblast - Bio::Tools::Run::PiseApplication::xblast Bio::Tools::Run::PiseApplication::blast2 - Bio::Tools::Run::PiseApplication::blast2 Bio::Tools::Run::PiseApplication::pepwindowall - Bio::Tools::Run::PiseApplication::pepwindowall Bio::Tools::Run::PiseApplication::infoalign - Bio::Tools::Run::PiseApplication::infoalign Bio::Tools::Run::PiseApplication::mfold - Bio::Tools::Run::PiseApplication::mfold Bio::Tools::Run::PiseApplication::primersearch - Bio::Tools::Run::PiseApplication::primersearch Bio::Tools::Run::PiseApplication::needle - Bio::Tools::Run::PiseApplication::needle Bio::Tools::Run::PiseApplication::geecee - Bio::Tools::Run::PiseApplication::geecee Bio::Tools::Run::PiseApplication::golden - Bio::Tools::Run::PiseApplication::golden Bio::Tools::Run::PiseApplication::eprimer3 - Bio::Tools::Run::PiseApplication::eprimer3 Bio::Tools::Run::PiseApplication::protal2dna - Bio::Tools::Run::PiseApplication::protal2dna Bio::Tools::Run::PiseApplication::digest - Bio::Tools::Run::PiseApplication::digest Bio::Tools::Run::PiseApplication::etandem - Bio::Tools::Run::PiseApplication::etandem Bio::Tools::Run::PiseApplication::matcher - Bio::Tools::Run::PiseApplication::matcher Bio::Tools::Run::PiseApplication::saps - Bio::Tools::Run::PiseApplication::saps Bio::Tools::Run::PiseApplication::showalign - Bio::Tools::Run::PiseApplication::showalign Bio::Tools::Run::PiseApplication::seqboot - Bio::Tools::Run::PiseApplication::seqboot Bio::Tools::Run::PiseApplication::dreg - Bio::Tools::Run::PiseApplication::dreg Bio::Tools::Run::PiseApplication::cirdna - Bio::Tools::Run::PiseApplication::cirdna Bio::Tools::Run::PiseApplication::revseq - Bio::Tools::Run::PiseApplication::revseq Bio::Tools::Run::PiseApplication::rnaga - Bio::Tools::Run::PiseApplication::rnaga Bio::Tools::Run::PiseApplication::recoder - Bio::Tools::Run::PiseApplication::recoder Bio::Tools::Run::PiseApplication::kitsch - Bio::Tools::Run::PiseApplication::kitsch Bio::Tools::Run::PiseApplication::banana - Bio::Tools::Run::PiseApplication::banana Bio::Tools::Run::PiseApplication::gb2xml - Bio::Tools::Run::PiseApplication::gb2xml Bio::Tools::Run::PiseApplication::tipdate - Bio::Tools::Run::PiseApplication::tipdate Bio::Tools::Run::PiseApplication::blimps - Bio::Tools::Run::PiseApplication::blimps Bio::Tools::Run::PiseApplication::pepstats - Bio::Tools::Run::PiseApplication::pepstats Bio::Tools::Run::PiseApplication::dssp - Bio::Tools::Run::PiseApplication::dssp Bio::Tools::Run::PiseApplication::polydot - Bio::Tools::Run::PiseApplication::polydot Bio::Tools::Run::PiseApplication::marscan - Bio::Tools::Run::PiseApplication::marscan Bio::Tools::Run::PiseApplication::protdist - Bio::Tools::Run::PiseApplication::protdist Bio::Tools::Run::PiseApplication::alistat - Bio::Tools::Run::PiseApplication::alistat Bio::Tools::Run::PiseApplication::decorate - Bio::Tools::Run::PiseApplication::decorate Bio::Tools::Run::PiseApplication::gff2ps - Bio::Tools::Run::PiseApplication::gff2ps Bio::Tools::Run::PiseApplication::trnascan - Bio::Tools::Run::PiseApplication::trnascan Bio::Tools::Run::PiseApplication::tfscan - Bio::Tools::Run::PiseApplication::tfscan Bio::Tools::Run::PiseApplication::bl2seq - Bio::Tools::Run::PiseApplication::bl2seq Bio::Tools::Run::PiseApplication::xpound - Bio::Tools::Run::PiseApplication::xpound Bio::Tools::Run::PiseApplication::hmmer2sam - Bio::Tools::Run::PiseApplication::hmmer2sam Bio::Tools::Run::PiseApplication::chaos - Bio::Tools::Run::PiseApplication::chaos Bio::Tools::Run::PiseApplication::pdbsearch - Bio::Tools::Run::PiseApplication::pdbsearch Bio::Tools::Run::PiseApplication::patmatdb - Bio::Tools::Run::PiseApplication::patmatdb Bio::Tools::Run::PiseApplication::dotmatcher - Bio::Tools::Run::PiseApplication::dotmatcher Bio::Tools::Run::PiseApplication::drawpyr - Bio::Tools::Run::PiseApplication::drawpyr Bio::Tools::Run::PiseApplication::emma - Bio::Tools::Run::PiseApplication::emma Bio::Tools::Run::PiseApplication::interface - Bio::Tools::Run::PiseApplication::interface Bio::Tools::Run::PiseApplication::charge - Bio::Tools::Run::PiseApplication::charge Bio::Tools::Run::PiseApplication::psiblast - Bio::Tools::Run::PiseApplication::psiblast Bio::Tools::Run::PiseApplication::fasta - Bio::Tools::Run::PiseApplication::fasta Bio::Tools::Run::PiseApplication::findkm - Bio::Tools::Run::PiseApplication::findkm Bio::Tools::Run::PiseApplication::sirna - Bio::Tools::Run::PiseApplication::sirna Bio::Tools::Run::PiseApplication::sam2hmmer - Bio::Tools::Run::PiseApplication::sam2hmmer Bio::Tools::Run::PiseApplication::boxshade - Bio::Tools::Run::PiseApplication::boxshade Bio::Tools::Run::PiseApplication::tacg - Bio::Tools::Run::PiseApplication::tacg Bio::Tools::Run::PiseApplication::rnapdist - Bio::Tools::Run::PiseApplication::rnapdist Bio::Tools::Run::PiseApplication::hmmsearch - Bio::Tools::Run::PiseApplication::hmmsearch Bio::Tools::Run::PiseApplication::weighbor - Bio::Tools::Run::PiseApplication::weighbor Bio::Tools::Run::PiseApplication::gibbs_scan - Bio::Tools::Run::PiseApplication::gibbs_scan Bio::Tools::Run::PiseApplication::blimps_block - Bio::Tools::Run::PiseApplication::blimps_block Bio::Tools::Run::PiseApplication::hmmpfam - Bio::Tools::Run::PiseApplication::hmmpfam Bio::Tools::Run::PiseApplication::redata - Bio::Tools::Run::PiseApplication::redata Bio::Tools::Run::PiseApplication::prettyseq - Bio::Tools::Run::PiseApplication::prettyseq Bio::Tools::Run::PiseApplication::clustalw - Bio::Tools::Run::PiseApplication::clustalw Bio::Tools::Run::PiseApplication::hmmscore - Bio::Tools::Run::PiseApplication::hmmscore Bio::Tools::Run::PiseApplication::seqmatchall - Bio::Tools::Run::PiseApplication::seqmatchall Bio::Tools::Run::PiseApplication::biosed - Bio::Tools::Run::PiseApplication::biosed Bio::Tools::Run::PiseApplication::prophecy - Bio::Tools::Run::PiseApplication::prophecy Bio::Tools::Run::PiseApplication::patser - Bio::Tools::Run::PiseApplication::patser Bio::Tools::Run::PiseApplication::grailclnt - Bio::Tools::Run::PiseApplication::grailclnt Bio::Tools::Run::PiseApplication::consensus - Bio::Tools::Run::PiseApplication::consensus Bio::Tools::Run::PiseApplication::chips - Bio::Tools::Run::PiseApplication::chips Bio::Tools::Run::PiseApplication::scope - Bio::Tools::Run::PiseApplication::scope Bio::Tools::Run::PiseApplication::compseq - Bio::Tools::Run::PiseApplication::compseq Bio::Tools::Run::PiseApplication::cpgplot - Bio::Tools::Run::PiseApplication::cpgplot Bio::Tools::Run::PiseApplication::coderet - Bio::Tools::Run::PiseApplication::coderet Bio::Tools::Run::PiseApplication::mview_blast - Bio::Tools::Run::PiseApplication::mview_blast Bio::Tools::Run::PiseApplication::rnasubopt - Bio::Tools::Run::PiseApplication::rnasubopt Bio::Tools::Run::PiseApplication::newcpgseek - Bio::Tools::Run::PiseApplication::newcpgseek Bio::Tools::Run::PiseApplication::distmat - Bio::Tools::Run::PiseApplication::distmat Bio::Tools::Run::PiseApplication::cai - Bio::Tools::Run::PiseApplication::cai Bio::Tools::Run::PiseApplication::cap - Bio::Tools::Run::PiseApplication::cap Bio::Tools::Run::PiseApplication::blimps_matrix - Bio::Tools::Run::PiseApplication::blimps_matrix Bio::Tools::Run::PiseApplication::cds - Bio::Tools::Run::PiseApplication::cds Bio::Tools::Run::PiseApplication::mview_alig - Bio::Tools::Run::PiseApplication::mview_alig Bio::Tools::Run::PiseApplication::wordmatch - Bio::Tools::Run::PiseApplication::wordmatch Bio::Tools::Run::PiseApplication::dan - Bio::Tools::Run::PiseApplication::dan Bio::Tools::Run::PiseApplication::readnexus - Bio::Tools::Run::PiseApplication::readnexus Bio::Toun::PiseApplication::sreformat - Bio::Tools::Run::PiseApplication::sreformat Bio::Tools::Run::PiseApplication::dsc - Bio::Tools::Run::PiseApplication::dsc Bio::Tools::Run::PiseApplication::tmap - Bio::Tools::Run::PiseApplication::tmap Bio::Tools::Run::PiseApplication::einverted - Bio::Tools::Run::PiseApplication::einverted Bio::Tools::Run::PiseApplication::phiblast - Bio::Tools::Run::PiseApplication::phiblast Bio::Tools::Run::PiseApplication::syco - Bio::Tools::Run::PiseApplication::syco Bio::Tools::Run::PiseApplication::most - Bio::Tools::Run::PiseApplication::most Bio::Tools::Run::PiseApplication::psort2 - Bio::Tools::Run::PiseApplication::psort2 Bio::Tools::Run::PiseApplication::notseq - Bio::Tools::Run::PiseApplication::notseq Bio::Tools::Run::PiseApplication::iep - Bio::Tools::Run::PiseApplication::iep Bio::Tools::Run::PiseApplication::trimest - Bio::Tools::Run::PiseApplication::trimest Bio::Tools::Run::PiseApplication::silent - Bio::Tools::Run::PiseApplication::silent Bio::Tools::Run::PiseApplication::stretcher - Bio::Tools::Run::PiseApplication::stretcher Bio::Tools::Run::PiseApplication::merger - Bio::Tools::Run::PiseApplication::merger Bio::Tools::Run::PiseApplication::getorf - Bio::Tools::Run::PiseApplication::getorf Bio::Tools::Run::PiseApplication::shuffleseq - Bio::Tools::Run::PiseApplication::shuffleseq Bio::Tools::Run::PiseApplication::mspcrunch - Bio::Tools::Run::PiseApplication::mspcrunch Bio::Tools::Run::PiseApplication::wordcount - Bio::Tools::Run::PiseApplication::wordcount Bio::Tools::Run::PiseApplication::emowse - Bio::Tools::Run::PiseApplication::emowse Bio::Tools::Run::PiseApplication::restover - Bio::Tools::Run::PiseApplication::restover Bio::Tools::Run::PiseApplication::genscan - Bio::Tools::Run::PiseApplication::genscan Bio::Tools::Run::PiseApplication::gruppi - Bio::Tools::Run::PiseApplication::gruppi Bio::Tools::Run::PiseApplication::comalign - Bio::Tools::Run::PiseApplication::comalign Bio::Tools::Run::PiseApplication::scan_for_matches - Bio::Tools::Run::PiseApplication::scan_for_matches Bio::Tools::Run::PiseApplication::water - Bio::Tools::Run::PiseApplication::water Bio::Tools::Run::PiseApplication::align2model - Bio::Tools::Run::PiseApplication::align2model Bio::Tools::Run::PiseApplication::vectorstrip - Bio::Tools::Run::PiseApplication::vectorstrip Bio::Tools::Run::PiseApplication::html4blast - Bio::Tools::Run::PiseApplication::html4blast Bio::Tools::Run::PiseApplication::codnocod - Bio::Tools::Run::PiseApplication::codnocod Bio::Tools::Run::PiseApplication::map - Bio::Tools::Run::PiseApplication::map Bio::Tools::Run::PiseApplication::hmmconvert - Bio::Tools::Run::PiseApplication::hmmconvert Bio::Tools::Run::PiseApplication::helixturnhelix - Bio::Tools::Run::PiseApplication::helixturnhelix Bio::Tools::Run::PiseApplication::prophet - Bio::Tools::Run::PiseApplication::prophet Bio::Tools::Run::PiseApplication::mix - Bio::Tools::Run::PiseApplication::mix Bio::Tools::Run::PiseApplication::lvb - Bio::Tools::Run::PiseApplication::lvb Bio::Tools::Run::PiseApplication::est2genome - Bio::Tools::Run::PiseApplication::est2genome Bio::Tools::Run::PiseApplication::pasteseq - Bio::Tools::Run::PiseApplication::pasteseq Bio::Tools::Run::PiseApplication::dollop - Bio::Tools::Run::PiseApplication::dollop Bio::Tools::Run::PiseApplication::freak - Bio::Tools::Run::PiseApplication::freak Bio::Tools::Run::PiseApplication::msa - Bio::Tools::Run::PiseApplication::msa Bio::Tools::Run::PiseApplication::qstar - Bio::Tools::Run::PiseApplication::qstar Bio::Tools::Run::PiseApplication::plotcon - Bio::Tools::Run::PiseApplication::plotcon Bio::Tools::Run::PiseApplication::wublast2 - Bio::Tools::Run::PiseApplication::wublast2 Bio::Tools::Run::PiseApplication::pestfind - Bio::Tools::Run::PiseApplication::pestfind Bio::Tools::Run::PiseApplication::toppred - Bio::Tools::Run::PiseApplication::toppred Bio::Tools::Run::PiseApplication::supermatcher - Bio::Tools::Run::PiseApplication::supermatcher Bio::Tools::Run::PiseApplication::stssearch - Bio::Tools::Run::PiseApplication::stssearch Bio::Tools::Run::PiseApplication::druid - Bio::Tools::Run::PiseApplication::druid Bio::Tools::Run::PiseApplication::repeats - Bio::Tools::Run::PiseApplication::repeats Bio::Tools::Run::PiseApplication::pam - Bio::Tools::Run::PiseApplication::pam Bio::Tools::Run::PiseApplication::diffseq - Bio::Tools::Run::PiseApplication::diffseq Bio::Tools::Run::PiseApplication::octanol - Bio::Tools::Run::PiseApplication::octanol Bio::Tools::Run::PiseApplication::pratt - Bio::Tools::Run::PiseApplication::pratt Bio::Tools::Run::PiseApplication::readseq - Bio::Tools::Run::PiseApplication::readseq Bio::Tools::Run::PiseApplication::prettyalign - Bio::Tools::Run::PiseApplication::prettyalign Bio::Tools::Run::PiseApplication::predator - Bio::Tools::Run::PiseApplication::predator Bio::Tools::Run::PiseApplication::checktrans - Bio::Tools::Run::PiseApplication::checktrans Bio::Tools::Run::PiseApplication::newcpgreport - Bio::Tools::Run::PiseApplication::newcpgreport Bio::Tools::Run::PiseApplication::sampleseqs - Bio::Tools::Run::PiseApplication::sampleseqs Bio::Tools::Run::PiseApplication::pyramids - Bio::Tools::Run::PiseApplication::pyramids Bio::Tools::Run::PiseApplication::hmmcalibrate - Bio::Tools::Run::PiseApplication::hmmcalibrate Bio::Tools::Run::PiseApplication::unroot - Bio::Tools::Run::PiseApplication::unroot Bio::Tools::Run::PiseApplication::hmmbuild - Bio::Tools::Run::PiseApplication::hmmbuild Bio::Tools::Run::PiseApplication::plsearch - Bio::Tools::Run::PiseApplication::plsearch Bio::Tools::Run::PiseApplication::showorf - Bio::Tools::Run::PiseApplication::showorf Bio::Tools::Run::PiseApplication::listor - Bio::Tools::Run::PiseApplication::listor Bio::Tools::Run::PiseApplication::homology - Bio::Tools::Run::PiseApplication::homology Bio::Tools::Run::PiseApplication::trimseq - Bio::Tools::Run::PiseApplication::trimseq Bio::Tools::Run::PiseApplication::pftools - Bio::Tools::Run::PiseApplication::pftools Bio::Tools::Run::PiseApplication::nrscope - Bio::Tools::Run::PiseApplication::nrscope Bio::Tools::Run::PiseApplication::wise2 - Bio::Tools::Run::PiseApplication::wise2 Bio::Tools::Run::PiseApplication::pars - Bio::Tools::Run::PiseApplication::pars Bio::Tools::Run::PiseApplication::sigscan - Bio::Tools::Run::PiseApplication::sigscan Bio::Tools::Run::PiseApplication::prettyplot - Bio::Tools::Run::PiseApplication::prettyplot Bio::Tools::Run::PiseApplication::dnapars - Bio::Tools::Run::PiseApplication::dnapars Bio::Tools::Run::PiseApplication::modelfromalign - Bio::Tools::Run::PiseApplication::modelfromalign Bio::Tools::Run::PiseApplication::showseq - Bio::Tools::Run::PiseApplication::showseq Bio::Tools::Run::PiseApplication::extractseq - Bio::Tools::Run::PiseApplication::extractseq Bio::Tools::Run::PiseApplication::rnainverse - Bio::Tools::Run::PiseApplication::rnainverse Bio::Tools::Run::PiseApplication::quicktree - Bio::Tools::Run::PiseApplication::quicktree Bio::Tools::Run::PiseApplication::prodom - Bio::Tools::Run::PiseApplication::prodom Bio::Tools::Run::PiseApplication::primo - Bio::Tools::Run::PiseApplication::primo Bio::Tools::Run::PiseApplication::dotpath - Bio::Tools::Run::PiseApplication::dotpath Bio::Tools::Run::PiseApplication::lindna - Bio::Tools::Run::PiseApplication::lindna Bio::Tools::Run::PiseApplication::seqstat - Bio::Tools::Run::PiseApplication::seqstat Bio::Tools::Run::PiseApplication::treealign - Bio::Tools::Run::PiseApplication::treealign Bio::Tools::Run::PiseApplication::codcmp - Bio::Tools::Run::PiseApplication::codcmp Bio::Tools::Run::PiseApplication::profit - Bio::Tools::Run::PiseApplication::profit Bio::Tools::Run::PiseApplication::loadseq - Bio::Tools::Run::PiseApplication::loadseq Bio::Tools::Run::PiseApplication::hmmalign - Bio::Tools::Run::PiseApplication::hmmalign Bio::Tools::Run::PiseApplication::clustalw_convert - Bio::Tools::Run::PiseApplication::clustalw_convert Bio::Tools::Run::PiseApplication::satellites - Bio::Tools::Run::PiseApplication::satellites Bio::Tools::Run::PiseApplication::plotorf - Bio::Tools::Run::PiseApplication::plotorf Bio::Tools::Run::PiseApplication::getblock - Bio::Tools::Run::PiseApplication::getblock Bio::Tools::Run::PiseApplication::codontree - Bio::Tools::Run::PiseApplication::codontree Bio::Tools::Run::PiseApplication::descseq - Bio::Tools::Run::PiseApplication::descseq Bio::Tools::Run::PiseApplication::pscan - Bio::Tools::Run::PiseApplication::pscan Bio::Tools::Run::PiseApplication::fmtseq - Bio::Tools::Run::PiseApplication::fmtseq Bio::Tools::Run::PiseApplication::mreps - Bio::Tools::Run::PiseApplication::mreps Bio::Tools::Run::PiseApplication::seqsblast - Bio::Tools::Run::PiseApplication::seqsblast Bio::Tools::Run::PiseApplication::environ - Bio::Tools::Run::PiseApplication::environ Bio::Tools::Run::PiseApplication::rnadistance - Bio::Tools::Run::PiseApplication::rnadistance Bio::Tools::Run::PiseApplication::prose - Bio::Tools::Run::PiseApplication::prose Bio::Tools::Run::PiseApplication::assp - Bio::Tools::Run::PiseApplication::assp Bio::Tools::Run::PiseApplication::restrict - Bio::Tools::Run::PiseApplication::restrict Bio::Tools::Run::PiseApplication::siggen - Bio::Tools::Run::PiseApplication::siggen Bio::Tools::Run::PiseApplication::drawtree - Bio::Tools::Run::PiseApplication::drawtree Bio::Tools::Run::PiseApplication::bambe - Bio::Tools::Run::PiseApplication::bambe Bio::Tools::Run::PiseApplication::neighbor - Bio::Tools::Run::PiseApplication::neighbor Bio::Tools::Run::PiseApplication::gibbs - Bio::Tools::Run::PiseApplication::gibbs Bio::Tools::Run::PiseApplication::oddcomp - Bio::Tools::Run::PiseApplication::oddcomp Bio::Tools::Run::PiseApplication::hmmemit - Bio::Tools::Run::PiseApplication::hmmemit Bio::Tools::Run::PiseApplication::con_filter - Bio::Tools::Run::PiseApplication::con_filter Bio::Tools::Run::PiseApplication::filtersites - Bio::Tools::Run::PiseApplication::filtersites Bio::Tools::Run::PiseApplication::tranalign - Bio::Tools::Run::PiseApplication::tranalign Bio::Tools::Run::PiseApplication::pepinfo - Bio::Tools::Run::PiseApplication::pepinfo Bio::Tools::Run::PiseApplication::nthseq - Bio::Tools::Run::PiseApplication::nthseq Bio::Tools::Run::PiseApplication::hmmfetch - Bio::Tools::Run::PiseApplication::hmmfetch Bio::Tools::Run::PiseApplication::pima - Bio::Tools::Run::PiseApplication::pima Bio::Tools::Run::PiseApplication::preg - Bio::Tools::Run::PiseApplication::preg Bio::Tools::Run::PiseApplication::palindrome - Bio::Tools::Run::PiseApplication::palindrome Bio::Tools::Run::PiseApplication::clique - Bio::Tools::Run::PiseApplication::clique Bio::Tools::Run::PiseApplication::btwisted - Bio::Tools::Run::PiseApplication::btwisted Bio::Tools::Run::PiseApplication::dottup - Bio::Tools::Run::PiseApplication::dottup Bio::Tools::Run::PiseApplication::msbar - Bio::Tools::Run::PiseApplication::msbar Bio::Tools::Run::PiseApplication::lassap - Bio::Tools::Run::PiseApplication::lassap Bio::Tools::Run::PiseApplication::abiview - Bio::Tools::Run::PiseApplication::abiview Bio::Tools::Run::PiseApplication::wobble - Bio::Tools::Run::PiseApplication::wobble Bio::Tools::Run::PiseApplication::seqgen - Bio::Tools::Run::PiseApplication::seqgen Bio::Tools::Run::PiseApplication::prot_nucml - Bio::Tools::Run::PiseApplication::prot_nucml Bio::Tools::Run::PiseApplication::codonw - Bio::Tools::Run::PiseApplication::codonw Bio::Tools::Run::PiseApplication::isochore - Bio::Tools::Run::PiseApplication::isochore Bio::Tools::Run::PiseApplication::maskseq - Bio::Tools::Run::PiseApplication::maskseq Bio::Tools::Run::PiseApplication::protpars - Bio::Tools::Run::PiseApplication::protpars Bio::Tools::Run::PiseApplication::twofeat - Bio::Tools::Run::PiseApplication::twofeat Bio::Tools::Run::PiseApplication::megamerger - Bio::Tools::Run::PiseApplication::megamerger Bio::Tools::Run::PiseApplication::showfeat - Bio::Tools::Run::PiseApplication::showfeat Bio::Tools::Run::PiseApplication::pepwheel - Bio::Tools::Run::PiseApplication::pepwheel Bio::Tools::Run::PiseApplication::equicktandem - Bio::Tools::Run::PiseApplication::equicktandem Bio::Tools::Run::PiseApplication::domainer - Bio::Tools::Run::PiseApplication::domainer Bio::Tools::Run::PiseApplication::drawgram - Bio::Tools::Run::PiseApplication::drawgram Bio::Tools::Run::PiseApplication::rnaeval - Bio::Tools::Run::PiseApplication::rnaeval Bio::Tools::Run::PiseApplication::parciquart - Bio::Tools::Run::PiseApplication::parciquart Bio::Tools::Run::PiseApplication::cpgreport - Bio::Tools::Run::PiseApplication::cpgreport Bio::Tools::Run::PiseApplication::fuzznuc - Bio::Tools::Run::PiseApplication::fuzznuc Bio::Tools::Run::PiseApplication::mwfilter - Bio::Tools::Run::PiseApplication::mwfilter Bio::Tools::Run::PiseApplication::sigcleave - Bio::Tools::Run::PiseApplication::sigcleave Bio::Tools::Run::PiseApplication::cutseq - Bio::Tools::Run::PiseApplication::cutseq Bio::Tools::Run::PiseApplication::extractfeat - Bio::Tools::Run::PiseApplication::extractfeat Bio::Tools::Run::PiseApplication::fuzzpro - Bio::Tools::Run::PiseApplication::fuzzpro Bio::Tools::Run::PiseApplication::pepwindow - Bio::Tools::Run::PiseApplication::pepwindow Bio::Tools::Run::PiseApplication::nnssp - Bio::Tools::Run::PiseApplication::nnssp Bio::Tools::Run::PiseApplication::newseq - Bio::Tools::Run::PiseApplication::newseq Bio::Tools::Run::PiseApplication::rnafold - Bio::Tools::Run::PiseApplication::rnafold Bio::Tools::Run::PiseApplication::maskfeat - Bio::Tools::Run::PiseApplication::maskfeat Bio::Tools::Run::PiseApplication::pepcoil - Bio::Tools::Run::PiseApplication::pepcoil Bio::Tools::Run::PiseApplication::CSR - Bio::Tools::Run::PiseApplication::CSR Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program Bio::Tools::Run::Alignment::Blat - Bio::Tools::Run::Blat Bio::Tools::Run::Alignment::Lagan - Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments) Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences Bio::Tools::Run::Alignment::TCoffee - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program Bio::Tools::Run::Alignment::DBA - Object for the alignment of two sequences using the DNA Block Aligner program. Bio::Tools::Run::Alignment::StandAloneFasta - Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3) Bio::Tools::Run::Analysis::soap - A SOAP-based access to the analysis tools Bio::Tools::Run::AnalysisFactory::Pise - A class to create Pise application objects. Bio::Tools::Run::AnalysisFactory::soap - A SOAP-based access to the list of analysis tools Bio::Tools::Sim4::Results - Results of one Sim4 run Bio::Tools::Sim4::Exon - A single exon determined by an alignment Bio::Tools::Blast::HSP - Bioperl BLAST High-Scoring Segment Pair object Bio::Tools::Blast::HTML - Bioperl Utility module for HTML formatting Blast reports Bio::Tools::Blast::Sbjct - Bioperl BLAST "Hit" object Bio::Tools::HMMER::Domain - One particular domain hit from HMMER Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches Bio::Tools::HMMER::Results - Object representing HMMER output results Bio::Tools::Phylo::Molphy - DESCRIPTION of Object Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 Bio::Tools::Phylo::PAML::Result - A PAML result set object Bio::Tools::Phylo::Molphy::Result - DESCRIPTION of Object Bio::Tools::Phylo::Phylip::ProtDist - DESCRIPTION of Object Bio::Tools::Alignment::Consed (0.60) - A module to work with objects from consed .ace files Bio::Tools::Alignment::Trim (0.01) - A kludge to do specialized trimming of sequence based on quality. Bio::Tools::Prediction::Exon - A predicted exon feature Bio::Tools::Prediction::Gene - a predicted gene structure feature Bio::Tools::StateMachine::IOStateMachine - IO-based implementation of AbstractStateMachine Bio::Tools::StateMachine::AbstractStateMachine - Abstract state machine object Bio::Tools::BPlite::HSP - Blast report High Scoring Pair (HSP) Bio::Tools::BPlite::Iteration - object for parsing single iteration of a PSIBLAST report Bio::Tools::BPlite::Sbjct - A Blast Subject (database search Hit) Bio::Matrix::PhylipDist - A Phylip Distance Matrix object Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events. Bio::SearchIO::chadosxpr - chadosxpr sequence input/output stream Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing Bio::SearchIO::chado - chado sequence input/output stream Bio::SearchIO::psiblast - Parser for traditional BLAST and PSI-BLAST reports Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events. Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing. Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program alignment output Bio::SearchIO::exonerate - parser for Exonerate Bio::SearchIO::hmmer - A parser for HMMER output (hmmpfam, hmmsearch) Bio::SearchIO::blast - Event generator for event based parsing of blast reports Bio::SearchIO::fasta - A SearchIO parser for FASTA results Bio::SearchIO::Writer::HitTableWriter - Tab-delimited data for Bio::Search::Hit::HitI objects Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each Bio::Search::Result::ResultI object. Bio::SearchIO::Writer::HSPTableWriter - Tab-delimited data for Bio::Search::HSP::HSPI objects Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text. Bio::SearchIO::Writer::HTMLResultWriter - Object to implement writing a Bio::Search::ResultI in HTML. Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects Bio::Search::DatabaseI - Interface for a database used in a sequence search Bio::Search::SearchUtils - Utility functions for Bio::Search:: objects Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI Bio::Search::Processor - DESCRIPTION of Object Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments Bio::Search::HSP::HMMERHSP - A HSP object for HMMER results Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits Bio::Search::Hit::HitI - Interface for a hit in a similarity search result Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects Bio::Search::Hit::BlastHit - Bioperl BLAST Hit object Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits Bio::Search::Result::WABAResult - Result object for WABA alignment output Bio::Search::Result::HMMERResult - A Result object for HMMER results Bio::Search::Result::ResultI - Abstract interface to Search Result objects Bio::Search::Result::BlastResult - A top-level BLAST Report object Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. Bio::Search::Result::ResultFactory - A factory to create Bio::Search::Result::ResultI objects Bio::Symbol::SymbolI - Interface for a Symbol Bio::Symbol::DNAAlphabet - A ready made DNA alphabet Bio::Symbol::Alphabet - DESCRIPTION of Object Bio::Symbol::AlphabetI - A Symbol Alphabet Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet Bio::Symbol::Symbol - A biological symbol Bio::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. Bio::TreeIO::newick - TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events Bio::ClusterIO::unigene - UniGene input stream Bio::ClusterIO::dbsnp - dbSNP input stream Bio::Ontology::Term - interface for ontology terms Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory Bio::Ontology::PathI - Interface for a path between ontology terms Bio::Ontology::TermFactory - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory Bio::Ontology::Path - a path for an ontology term graph Bio::Ontology::GOterm - representation of GO terms Bio::Ontology::Ontology - standard implementation of an Ontology Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface Bio::Ontology::InterProTerm - Implementation of InterProI term interface Bio::Ontology::OntologyI - Interface for an ontology implementation Bio::Ontology::Relationship - a relationship for an ontology Bio::Ontology::OntologyStore - A repository of ontologies Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms Bio::Ontology::TermI - interface for ontology terms Bio::Ontology::SimpleGOEngine - a Ontology Engine for GO implementing OntologyEngineI Bio::Ontology::RelationshipType - a relationship type for an ontology Bio::Cluster::UniGeneI (1.0) - abstract interface of UniGene object Bio::Cluster::SequenceFamily - Sequence Family object Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory Bio::Cluster::FamilyI - Family Interface Bio::Cluster::UniGene - UniGene object Bio::Location::WidestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence Bio::Location::NarrowestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points) Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise Bio::Location::Simple - Implementation of a Simple Location on a Sequence Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points) Bio::Taxonomy::Taxon - Generic Taxonomic Entity object Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface. Bio::Coordinate::Pair - Continuous match between two coordinate sets Bio::Coordinate::Result - Results from coordinate transformation Bio::Coordinate::MapperI - Interface describing coordinate mappers Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects Bio::Coordinate::ResultI - Interface to identify coordinate mapper results Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets Bio::Coordinate::GeneMapper - transformations between gene related coordinate systems Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets Bio::Coordinate::Graph - Finds shortest path between nodes in a graph Bio::Coordinate::Result::Gap - An other name for Bio::Location::Simple Bio::Coordinate::Result::Match - An other name for Bio::Location::Simple Bio::LiveSeq::DNA (1.4) - DNA object for LiveSeq Bio::LiveSeq::Range (1.6) - Range abstract class for LiveSeq Bio::LiveSeq::Repeat_Unit (1) - Repeat_Unit class for LiveSeq Bio::LiveSeq::Repeat_Region (1) - Repeat_Region class for LiveSeq Bio::LiveSeq::Mutator - Package mutating LiveSequences Bio::LiveSeq::Mutation - Mutation event descriptor class Bio::LiveSeq::SeqI (3.3) - Abstract sequence interface class for LiveSeq Bio::LiveSeq::Intron (1) - Range abstract class for LiveSeq Bio::LiveSeq::Exon (1.1) - Range abstract class for LiveSeq Bio::LiveSeq::ChainI (1.9) - Double linked chain data structure Bio::LiveSeq::Gene (2.3) - Range abstract class for LiveSeq Bio::LiveSeq::Prim_Transcript (1) - Prim_Transcript class for LiveSeq Bio::LiveSeq::Transcript (5.2) - Transcript class for LiveSeq Bio::LiveSeq::Translation (1.8) - Translation class for LiveSeq Bio::LiveSeq::Chain (2.7) - DoubleChain DataStructure for Perl Bio::LiveSeq::AARange (1.8) - AARange abstract class for LiveSeq Bio::LiveSeq::IO::Loader (4.44) - Parent Loader for LiveSeq Bio::LiveSeq::IO::SRS - Loader for LiveSeq from EMBL entries with SRS Bio::LiveSeq::IO::BioPerl (2.42) - Loader for LiveSeq from EMBL entries with BioPerl Bio::Assembly::Contig - Perl module to hold and manipulate sequence assembly contigs. Bio::Assembly::IO - Handler for Assembly::IO Formats Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies Bio::Assembly::Scaffold (0.0.1) - Perl module to hold and manipulate sequence assembly data. Bio::Assembly::ContigAnalysis - Perform analysis on sequence assembly contigs. Bio::Assembly::IO::phrap - driver to load phrap.out files. Bio::Assembly::IO::ace - module to load phrap ACE files. Bio::Annotation::StructuredValue - A scalar with embedded structured information Bio::Annotation::Reference - Specialised DBLink object for Literature References Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI Bio::Annotation::TypeManager - Manages types for annotation collections Bio::Annotation::DBLink - DESCRIPTION of Object Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory Bio::Annotation::SimpleValue - A simple scalar Bio::Annotation::Comment - A comment object, holding text Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI Bio::OntologyIO::InterProParser - Parser for InterPro xml files. Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format Bio::OntologyIO::Handlers::InterProHandler - XML handler class for InterProParser Bio::Factory::SequenceProcessorI - Interface for chained sequence processing algorithms Bio::Factory::ObjectBuilderI - Interface for an object builder Bio::Factory::BlastHitFactory - Factory for Bio::Search::Hit::BlastHit objects Bio::Factory::BlastResultFactory - Factory for Bio::Search::Result::BlastResult objects Bio::Factory::ObjectFactoryI - A General object creator factory Bio::Factory::FTLocationFactory - A FeatureTable Location Parser Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees from/to a data stream Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory Bio::Factory::ResultFactoryI - Interface for an object that builds Bio::Search::Result::ResultI objects Bio::Factory::DriverFactory - Base class for factory classes loading drivers Bio::Factory::LocationFactoryI - DESCRIPTION of Interface Bio::Factory::HitFactoryI - Interface for an object that builds Bio::Search::Hit::HitI objects Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream. Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO) Bio::Factory::MapFactoryI - A Factory for getting markers Bio::Factory::ApplicationFactoryI - Interface class for Application Factories Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers Bio::Factory::AnalysisI - An interface to analysis tool factory Bio::Factory::EMBOSS - EMBOSS appliaction factory class Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel Bio::Graphics::Panel - Generate GD images of Bio::Seq objects Bio::Graphics::Browser (1.15) - Utility methods for the Generic Genome Browser Bio::Graphics::Glyph - Base class for Bio::Graphics::Glyph objects Bio::Graphics::Browser::Plugin (0.20) - Base class for gbrowse plugins. Bio::Graphics::Browser::Realign - Perl extension for Smith-Waterman alignments Bio::Graphics::Browser::Util - Exported utilities Bio::Graphics::Browser::Markup - Markup routines for sequences in text form Bio::Graphics::Browser::PadAlignment - Insert pads into a multiple alignment Bio::Graphics::Glyph::ex - The "crossbox" glyph Bio::Graphics::Glyph::segmented_keyglyph - The "segmented_keyglyph" glyph Bio::Graphics::Glyph::line - The "line" glyph Bio::Graphics::Glyph::span - The "span" glyph Bio::Graphics::Glyph::ruler_arrow - The "ruler_arrow" glyph Bio::Graphics::Glyph::redgreen_segment - The "redgreen_segments" glyph Bio::Graphics::Glyph::dna - The "dna" glyph Bio::Graphics::Glyph::group - The "group" glyph Bio::Graphics::Glyph::pinsertion - The "Drosophila P-element Insertion" glyph Bio::Graphics::Glyph::rndrect - The "round rect" glyph Bio::Graphics::Glyph::cds - The "cds" glyph Bio::Graphics::Glyph::box - The "box" glyph Bio::Graphics::Glyph::primers - The "STS primers" glyph Bio::Graphics::Glyph::segments - The "segments" glyph Bio::Graphics::Glyph::dot - The "dot" glyph Bio::Graphics::Glyph::diamond - The "diamond" glyph Bio::Graphics::Glyph::ellipse - The "ellipse" glyph Bio::Graphics::Glyph::transcript - The "transcript" glyph Bio::Graphics::Glyph::anchored_arrow - The "anchored_arrow" glyph Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects Bio::Graphics::Glyph::xyplot - The xyplot glyph Bio::Graphics::Glyph::extending_arrow - The "extending arrow" glyph Bio::Graphics::Glyph::triangle - The "triangle" glyph Bio::Graphics::Glyph::arrow - The "arrow" glyph Bio::Graphics::Glyph::alignment - The "alignment" glyph Bio::Graphics::Glyph::oval - The "oval" glyph Bio::Graphics::Glyph::transcript2 - The "transcript2" glyph Bio::Graphics::Glyph::heterogeneous_segments - The "heterogeneous_segments" glyph Bio::Graphics::Glyph::track - The "track" glyph Bio::Graphics::Glyph::wormbase_transcript (1.03) - The "wormbase_transcript" glyph Bio::Graphics::Glyph::insertion_chromosome - The "insertion_chromosome" glyph Bio::Graphics::Glyph::redgreen_box - The "redgreen_box" glyph Bio::Graphics::Glyph::splice_site - The "splice_site" glyph Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph Bio::Graphics::Glyph::toomany - The "too many to show" glyph Bio::Graphics::Glyph::crossbox - The "crossbox" glyph Bio::Graphics::Glyph::translation - The "6-frame translation" glyph Bio::Graphics::Glyph::graded_segments - The "graded_segments" glyph Bio::Graphics::Glyph::generic - The "generic" glyph Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature Bio::SeqFeature::Similarity - A sequence feature based on similarity Bio::SeqFeature::Primer - Primer Generic SeqFeature Bio::SeqFeature::Computation - Computation SeqFeature 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. Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences. Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects. Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits Bio::SeqFeature::Generic - Generic SeqFeature Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region that is part of a transcription unit Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene Bio::SeqFeature::Gene::Promoter - Describes a promotor Bio::SeqFeature::Gene::Poly_A_site - DESCRIPTION of Object Bio::SeqFeature::Gene::NC_Feature - DESCRIPTION of Object Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon Bio::SeqFeature::Gene::Intron - DESCRIPTION of Object Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene Bio::SeqFeature::Gene::Exon - a feature representing an exon Bio::SeqFeature::Gene::Transcript - A feature representing a transcript Bio::Structure::Model - Bioperl structure Object, describes a Model Bio::Structure::IO - Handler for Structure Formats Bio::Structure::Atom - Bioperl structure Object, describes an Atom Bio::Structure::Entry - Bioperl structure Object, describes the whole entry Bio::Structure::StructureI - Abstract Interface for a Structure objects Bio::Structure::Residue - Bioperl structure Object, describes a Residue Bio::Structure::Chain - Bioperl structure Object, describes a chain Bio::Structure::IO::pdb - PDB input/output stream Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes Bio::Phenotype::Phenotype - A class for modeling phenotypes Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database Bio::Phenotype::OMIM::MiniMIMentry - Representation of a Mini MIM entry Bio::Variation::AAReverseMutate - point mutation and codon information from single amino acid changes Bio::Variation::IO - Handler for sequence variation IO Formats Bio::Variation::SNP - submitted SNP Bio::Variation::DNAMutation - DNA level mutation class Bio::Variation::SeqDiff - Container class for mutation/variant descriptions Bio::Variation::Allele - Sequence object with allele-specific attributes Bio::Variation::AAChange - Sequence change class for polypeptides Bio::Variation::VariantI (1) - Sequence Change SeqFeature abstract class Bio::Variation::RNAChange - Sequence change class for RNA level Bio::Variation::IO::flat - flat file sequence variation input/output stream Bio::Variation::IO::xml - XML sequence variation input/output stream Heap::Binomial (0.01) - a Perl extension for keeping data partially sorted Heap::Elem (0.01) - Perl extension for elements to be put in Heaps Heap::Binary (0.01) - a Perl extension for keeping data partially sorted Heap::Fibonacci (0.01) - a Perl extension for keeping data partially sorted Heap::Elem::RefRev (0.01) - Perl extension for reversed Object Reverence Heap Elements Heap::Elem::Num (0.01) - Perl extension for Numeric Heap Elements Heap::Elem::Ref (0.01) - Perl extension for Object Reference Heap Elements Heap::Elem::Str (0.01) - Perl extension for String Heap Elements Heap::Elem::NumRev (0.01) - Perl extension for Reversed Numeric Heap Elements Heap::Elem::StrRev (0.01) - Perl extension for Reversed String Heap Elements Graph::HeapElem (0.01) - internal use only Graph::Base - graph base class Graph::Traversal - graph traversal Graph::Directed - directed graphs Graph::Undirected - directed graphs Graph::BFS - graph breadth-first search Graph::DFS - graph depth-first search Data::Grove (0.07) - support for deeply nested structures Data::TemporaryBag (0.06) - Handle long size data using temporary file . Data::Stag (0.03) - Structured Tags datastructures Data::Stag::SxprWriter (0.03) - Data::Stag::SxprWriter Data::Stag::SxprParser (0.03) - simple wrapper for lisp style S-expression Data::Stag::XMLWriter (0.03) - Data::Stag::XMLWriter Data::Stag::ChainHandler (0.03) - Data::Stag::ChainHandler Data::Stag::SAX2Stag - Data::Stag::SAX2Stag Data::Stag::XMLParser (0.03) - simple wrapper for Data::Stag::Simple (0.03) - Data::Stag::Simple Data::Stag::ITextWriter (0.03) - Data::Stag::ITextWriter Data::Stag::ITextParser (0.03) - simple wrapper for Data::Stag::Arr2HTML (0.03) - Data::Stag::Arr2HTML Data::Stag::BaseGenerator - base class for parsers Data::Stag::Writer (0.03) - Data::Stag::Writer Data::Stag::null (0.03) - Data::Stag::Arr2HTML Data::Stag::GraphWriter (0.03) - Data::Stag::GraphWriter Data::Stag::BaseHandler (0.03) - Base class for writing tag stream handlers Data::Stag::StagImpl (0.03) - Data::Stag::StagImpl Data::Grove::Visitor (0.07) - add visitor/callback methods to Data::Grove objects Data::Grove::Parent (0.07) - provide parent properties to Data::Grove objects Text::Shellwords (1.02) - Text::Shellwords XML::Twig (3.11) - A perl module for processing huge XML documents in tree mode. XML::ESISParser (0.07) - Perl SAX parser using nsgmls 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::Writer (0.4) - Perl extension for writing XML documents. XML::Node (0.11) - XML::RegExp (0.02) - Regular expressions for XML tokens XML::DOM (1.43) - A perl module for building DOM Level 1 compliant document structures XML::DOM::PerlSAX - Old name of L XML::SAX::Base (1.02) - Base class SAX Drivers and Filters XML::SAX::Exception (1.01) - Exception classes for XML::SAX 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 XML::PatAct::ActionTempl - An action module for XML::PatAct::MatchName (0.07) - A pattern module for matching element names XML::Handler::CanonXMLWriter (0.07) - output XML in canonical XML format XML::Handler::XMLWriter (0.07) - a PerlSAX handler for writing readable XML XML::Handler::Sample - a trivial PerlSAX handler XML::Handler::Subs (0.07) - a PerlSAX handler base class for calling user-defined subs XML::Handler::BuildDOM - PerlSAX handler that creates XML::DOM document structures XML::Parser::Lite (0.55) - Lightweight regexp-based XML parser XML::Parser::PerlSAX (0.07) - Perl SAX parser using XML::Parser Apache::SOAP - mod_perl-based SOAP server with minimum configuration Apache::XMLRPC::Lite - mod_perl-based XML-RPC server with minimum configuration SOAP::Lite (0.55) - Client and server side SOAP implementation SOAP::Test (0.55) - Test framework for SOAP::Lite SOAP::Transport::FTP (0.55) - Client side FTP support for SOAP::Lite SOAP::Transport::MAILTO (0.55) - Client side SMTP/sendmail support for SOAP::Lite SOAP::Transport::IO (0.55) - Server side IO support for SOAP::Lite SOAP::Transport::MQ - Server/Client side MQ support for SOAP::Lite SOAP::Transport::TCP (0.55) - Server/Client side TCP support for SOAP::Lite SOAP::Transport::JABBER - Server/Client side JABBER support for SOAP::Lite SOAP::Transport::LOCAL (0.55) - Client side no-transport support for SOAP::Lite SOAP::Transport::HTTP (0.55) - Server/Client side HTTP support for SOAP::Lite SOAP::Transport::POP3 (0.55) - Server side POP3 support for SOAP::Lite UDDI::Lite (0.55) - Library for UDDI clients in Perl XMLRPC::Lite (0.55) - client and server implementation of XML-RPC protocol XMLRPC::Test (0.55) - Test framework 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 XMLRPC::Transport::POP3 (0.55) - Server side POP3 support for XMLRPC::Lite MIME::Lite (3.01) - low-calorie MIME generator IO::Scalar (2.104) - IO:: interface for reading/writing a scalar IO::Stringy (2.108) - I/O on in-core objects like strings and arrays IO::Wrap (2.102) - wrap raw filehandles in IO::Handle interface IO::AtomicFile (2.101) - write a file which is updated atomically IO::WrapTie (2.102) - wrap tieable objects in IO::Handle interface IO::ScalarArray (2.103) - IO:: interface for reading/writing an array of scalars IO::InnerFile (2.102) - define a file inside another file IO::Lines (2.103) - IO:: interface for reading/writing an array of lines IO::String (1.03) - Emulate file interface for in-core strings IO::Socket::SSL (0.95) - Nearly transparent SSL encapsulation for IO::Socket::INET. GD (2.11) - Interface to Gd Graphics Library Ace (1.86) - Object-Oriented Access to ACEDB Databases DBI (1.37) - Database independent interface for Perl Mysql (1.2401) - Perl interfaces to the mSQL and mysql databases Oraperl (1.43) - Perl access to Oracle databases for old oraperl scripts Text::Iconv (1.2) - Perl interface to iconv() codeset conversion function String::Approx (3.20) - Perl extension for approximate matching (fuzzy matching) Term::ReadKey (2.21) - A perl module for simple terminal control Data::Dumper (2.121) - stringified perl data structures, suitable for both printing and C Compress::Zlib (1.31) - Interface to zlib compression library Net::SSLeay (1.25) - Perl extension for using OpenSSL Net::SSLeay::Handle (0.61) - Perl module that lets SSL (HTTPS) sockets be handled as standard file handles. WWW::Curl (2.0) - Perl extension interface for libcurl WWW::Curl::easy (2.0) - Perl extension interface for libcurl Curl::easy (1.36) - Compatability Perl extension interface for libcurl HTML::TokeParser (2.28) - Alternative HTML::Parser interface HTML::HeadParser (2.18) - Parse section of a HTML document HTML::PullParser (2.07) - Alternative HTML::Parser interface HTML::Parser (3.34) - HTML parser class HTML::Filter (2.10) - Filter HTML text through the parser HTML::LinkExtor (1.33) - Extract links from an HTML document HTML::Entities (1.27) - Encode or decode strings with HTML entities Params::ValidatePP - pure Perl implementation of Params::Validate Params::ValidateXS - XS implementation of Params::Validate Params::Validate (0.62) - Validate method/function parameters Attribute::Params::Validate (1.07) - Validate method/function parameters using attributes DBD::Proxy - A proxy driver for the DBI DBD::Oracle (1.14) - Oracle database driver for the DBI module DBI::FAQ (0.38) - The Frequently Asked Questions for the Perl5 Database Interface DBI::Profile (1.06) - Performance profiling and benchmarking for the DBI DBI::ProxyServer - a server for the DBD::Proxy driver DBI::ProfileData (1.0) - manipulate DBI::ProfileDumper data dumps DBI::PurePerl (1.95) - a DBI emulation using pure perl (no C/XS compilation required) DBI::Changes - List of significant changes to the DBI DBI::ProfileDumper (1.0) - profile DBI usage and output data to a file DBI::W32ODBC - An experimental DBI emulation layer for Win32::ODBC DBI::DBD (11.16) - Perl DBI Database Driver Writer's Guide DBI::DBD::Metadata - Generate the code and data for some DBI metadata methods DBI::Const::GetInfoType - Data describing GetInfo type codes DBI::Const::GetInfoReturn - Data and functions for describing GetInfo results DBI::Const::GetInfo::ODBC - ODBC Constants for GetInfo DBI::Const::GetInfo::ANSI - ISO/IEC SQL/CLI Constants for GetInfo DBI::ProfileDumper::Apache (1.0) - capture DBI profiling data from Apache/mod_perl Bundle::DBI (11.03) - A bundle to install DBI and required modules. Bundle::DBD::mysql (2.0416) - A bundle to install Perl drivers for mSQL or MySQL Win32::DBIODBC - Win32::ODBC emulation layer for the DBI 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::Debug - Debug style for XML::Parser XML::Parser::Style::Objects - XML::Parser::Style::Objects XML::Parser::Style::Stream - Stream style for XML::Parser XML::Parser::Style::Subs - XML::Parser::Style::Subs XML::Parser::Style::Tree - XML::Parser::Style::Tree Ace::Model (1.51) - Get information about AceDB models Ace::Iterator (1.51) - Iterate Across an ACEDB Query Ace::Object (1.66) - Manipulate Ace Data Objects Ace::Local (1.05) - use giface, tace or gifaceclient to open a local connection to an Ace database Ace::Sequence (1.51) - Examine ACeDB Sequence Objects Ace::Browser::AceSubs - Subroutines for AceBrowser Ace::Browser::SearchSubs - Subroutines for AceBrowser search scripts Ace::Browser::SiteDefs - Access to AceBrowser configuration files Ace::Sequence::Multi - Combine Feature Tables from Multiple Databases Ace::Sequence::Homol - Temporary Sequence Homology Class Ace::Sequence::GappedAlignment (1.20) - Gapped alignment object Ace::Sequence::FeatureList - Lightweight Access to Features Ace::Sequence::Feature - Examine Sequence Feature Tables Ace::Sequence::Gene - Simple "Gene" Object Ace::Sequence::Transcript - Simple "Gene" Object Ace::Graphics::GlyphFactory - Create Ace::Graphics::Glyphs Ace::Graphics::Fk - A dummy feature object used for generating panel key tracks Ace::Graphics::Glyph - Base class for Ace::Graphics::Glyph objects Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects Ace::Graphics::Panel - PNG graphics of Ace::Sequence::Feature objects Ace::Graphics::Glyph::ex - The "X" glyph Ace::Graphics::Glyph::toomany - The "too many to show" glyph Ace::Graphics::Glyph::line - The "line" glyph Ace::Graphics::Glyph::group - The group glyph Ace::Graphics::Glyph::span - The "span" glyph Ace::Graphics::Glyph::box - The "box" glyph Ace::Graphics::Glyph::graded_segments - The "color-coded segments" glyph Ace::Graphics::Glyph::dot - The "ellipse" glyph Ace::Graphics::Glyph::primers - The "STS primers" glyph Ace::Graphics::Glyph::segments - The "discontinuous segments" glyph Ace::Graphics::Glyph::transcript - The "gene" glyph Ace::Graphics::Glyph::anchored_arrow - The "anchored_arrow" glyph Ace::Graphics::Glyph::triangle - The "triangle" glyph Ace::Graphics::Glyph::arrow - The "arrow" glyph GD::Polyline (0.1) - Polyline object and Polygon utilities (including splines) for use with GD Cwd (2.06) - get pathname of current working directory Config - access Perl configuration information lib (0.5564) - manipulate @INC at compile time re (0.03) - Perl pragma to alter regular expression behaviour XSLoader (0.01) - Dynamically load C libraries into Perl code DynaLoader (1.04) - Dynamically load C libraries into Perl code attrs (1.01) - set/get attributes of a subroutine (deprecated) ByteLoader (0.04) - load byte compiled perl code B (1.01) - The Perl Compiler O (1.00) - Generic interface to Perl Compiler backends Fcntl (1.04) - load the C Fcntl.h defines Encode (1.75) - character encodings encoding (1.35) - allows you to write your script in non-ascii or non-utf8 GDBM_File (1.06) - Perl5 access to the gdbm library. IO (1.20) - load various IO modules NDBM_File (1.04) - Tied access to ndbm files Safe (2.07) - Compile and execute code in restricted compartments ops (1.00) - Perl pragma to restrict unsafe operations when compiling Opcode (1.05) - Disable named opcodes when compiling perl code SDBM_File (1.03) - Tied access to sdbm files Socket (1.75) - load the C socket.h defines and structure manipulators threads (0.99) - Perl extension allowing use of interpreter based threads from perl Errno (1.09) - System errno constants DB_File (1.806) - Perl5 access to Berkeley DB version 1.x Storable (2.08) - persistence for Perl data structures List::Util - A selection of general-utility list subroutines Scalar::Util - A selection of general-utility scalar subroutines Devel::DProf - a Perl code profiler Devel::Peek (1.0003) - A data debugging tool for the XS programmer Devel::PPPort (2.0002) - Perl/Pollution/Portability File::Glob (1.01) - Perl extension for BSD glob routine Filter::Util::Call (1.06) - Perl Source Filter Utility Module I18N::Langinfo (0.01) - query locale information IPC::Msg (1) - SysV Msg IPC object class IPC::Semaphore (1) - SysV Semaphore IPC object class IPC::SysV (1.03) - SysV IPC constants PerlIO::encoding (0.06) - encoding layer PerlIO::scalar (0.01) - support module for in-memory IO. PerlIO::via (0.01) - Helper class for PerlIO layers implemented in perl Time::HiRes (1.2) - High resolution alarm, sleep, gettimeofday, interval timers Unicode::Normalize (0.17) - Unicode Normalization Forms B::Deparse (0.63) - Perl compiler backend to produce perl code B::Lint (1.01) - Perl lint B::Stash (-umain,-uutf8,-uattributes,-uPerlIO,-uPerlIO::Layer,-uInternals,-uDB 1.00) - show what stashes are loaded B::Asmdata (1.00) - Autogenerated data about Perl ops, used to generate bytecode B::C - Perl compiler's C backend B::Concise (0.52) - Walk Perl syntax tree, printing concise info about ops B::Debug (1.00) - Walk Perl syntax tree, printing debug info about ops B::Bytecode (1.00) - Perl compiler's bytecode backend B::Showlex (1.00) - Show lexical variables used in functions or files B::Disassembler - Disassemble Perl bytecode B::Bblock (1.00) - Walk basic blocks B::Terse (1.00) - Walk Perl syntax tree, printing terse info about ops B::Assembler (0.04) - Assemble Perl bytecode B::Xref (1.01) - Generates cross reference reports for Perl programs B::CC (1.00) - Perl compiler's optimized C translation backend B::Stackobj (1.00) - Helper module for CC backend Data::Dumper (2.121) - stringified perl data structures, suitable for both printing and C Digest::MD5 (2.30) - Perl interface to the MD5 Algorithm Encode::Alias (1.32) - alias definitions to encodings Encode::Encoding (1.30) - Encode Implementation Base Class Encode::Config (1.06) - internally used by Encode Encode::Guess (1.06) - Guesses encoding from data Encode::Encoder (0.05) - Object Oriented Encoder Encode::CJKConstants (1.00) - Internally used by Encode::??::ISO_2022_* Encode::Byte (1.22) - 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 (1.22) - Korean Encodings Encode::Symbol (1.22) - Symbol Encodings Encode::TW (1.26) - Taiwan-based Chinese Encodings Encode::Unicode (1.37) - Various Unicode Transformation Formats IO::Pipe (1.122) - supply object methods for pipes IO::Handle (1.21) - supply object methods for I/O handles IO::File (1.09) - supply object methods for filehandles IO::Socket (1.27) - Object interface to socket communications IO::Select (1.15) - OO interface to the select system call IO::Poll (0.06) - Object interface to system poll call IO::Dir (1.03) - supply object methods for directory handles IO::Seekable (1.08) - supply seek based methods for I/O objects MIME::Base64 (2.21) - Encoding and decoding of base64 strings MIME::QuotedPrint (2.21) - Encoding and decoding of quoted-printable strings Sys::Hostname (1.1) - Try every conceivable way to get hostname Sys::Syslog (0.03) - Perl interface to the UNIX syslog(3) calls threads::shared (0.90) - Perl extension for sharing data structures between threads XS::APItest (0.01) - Test the perl C API XS::Typemap (0.01) - module to test the XS typemaps distributed with perl