Hunter Patch Adams Bio
OpenSSH Heartbeat/Watchdog Patch adds a heartbeat (keepalive) function to ssh(1). If the output channel has been silent for more than a specified time, a null message (SSH_MSG_IGNORE) is sent to the server as a heartbeat. The heartbeat is useful for keeping connections over IP masquerade/NAT...
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License: Freeware | Size: 8.19 KB | Download (102): OpenSSH Heartbeat/Watchdog Patch Download |
Bio::Ontology::Ontology is a standard implementation of an Ontology. SYNOPSIS use Bio::Ontology::Ontology; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-name => "Bioperl"); my $obf =...
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License: Freeware | Size: 4.7 MB | Download (92): Bio::Ontology::Ontology Download |
Bio::Factory::SeqAnalysisParserFactoryI is a Perl interface describing objects capable of creating SeqAnalysisParserI compliant parsers. SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object...
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License: Freeware | Size: 4.7 MB | Download (97): Bio::Factory::SeqAnalysisParserFactoryI Download |
Bio::Location::CoordinatePolicyI is an abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location. SYNOPSIS # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print...
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Bio::Tools::Run::PiseApplication::freak is a Perl module. Bio::Tools::Run::PiseApplication::freak Bioperl class for: FREAK Residue/base frequency table or plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/freak.html for available values): freak...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (94): Bio::Tools::Run::PiseApplication::freak Download |
Bio::MAGE::Protocol::SoftwareApplication is a Perl module. SYNOPSIS use Bio::MAGE::Protocol::SoftwareApplication; # creating an empty instance my $softwareapplication = Bio::MAGE::Protocol::SoftwareApplication->new(); # creating an already populated instance my $softwareapplication =...
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License: Freeware | Size: 460.8 KB | Download (92): Bio::MAGE::Protocol::SoftwareApplication Download |
Bio::MAGE::Protocol::Software - Software represents the software used. SYNOPSIS use Bio::MAGE::Protocol::Software; # creating an empty instance my $software = Bio::MAGE::Protocol::Software->new(); # creating an already populated instance my $software =...
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License: Freeware | Size: 460.8 KB | Download (148): Bio::MAGE::Protocol::Software Download |
Bio::Genex::Software is Perl module with methods for processing data from the GeneX DB table: Software. SYNOPSIS use Bio::Genex::Software; # instantiating an instance my $Software = Bio::Genex::Software->new(id=>47); # retrieve data from the DB for all columns $Software->fetch(); #...
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License: Freeware | Size: 552.96 KB | Download (107): Bio::Genex::Software Download |
Bio::PopGen::IO contains input individual,marker,allele information. SYNOPSIS use Bio::PopGen::IO; my $io = new Bio::PopGen::IO(-format => csv, -file => data.csv); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (104): Bio::PopGen::IO Download |
Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. SYNOPSIS use Bio::Tree::DistanceFactory; use Bio::AlignIO; use Bio::Align::DNAStatistics; my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ"); my $stats =...
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License: Freeware | Size: 5.6 MB | Download (95): Bio::Tree::DistanceFactory Download |
Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s). SYNOPSIS use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1);...
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License: Freeware | Size: 4.7 MB | Download (97): Bio::Index::Blast Download |
Bio::Map::MappableI is an object that can be placed in a map. SYNOPSIS # get a Bio::Map::MappableI somehow my $position = $element->map_position(); # these methods will be important for building sorted lists if( $position->equals($p2) ) { # do something } elsif( $position->less_tha($p2)...
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License: Freeware | Size: 4.7 MB | Download (109): Bio::Map::MappableI Download |
Bio::Tree::Tree is an implementation of TreeI interface. SYNOPSIS # like from a TreeIO my $treeio = new Bio::TreeIO(-format => newick, -file => treefile.dnd); my $tree = $treeio->next_tree; my @nodes = $tree->get_nodes; my $root = $tree->get_root_node; This object holds handles to Nodes...
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License: Freeware | Size: 4.7 MB | Download (142): Bio::Tree::Tree Download |
Bio::Factory::SequenceFactoryI is a Perl interface that allows for generic building of sequences in factories which create sequences (like SeqIO). SYNOPSIS # do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like use Bio::Seq::SeqFactory; my...
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License: Freeware | Size: 4.7 MB | Download (102): Bio::Factory::SequenceFactoryI Download |
Bio::LiveSeq::Translation is a translation class for LiveSeq. This stores informations about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate...
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License: Freeware | Size: 4.7 MB | Download (104): Bio::LiveSeq::Translation Download |
Bio::Tools::Run::JavaRunner is a Perl module that can run java programs. SYNOPSIS my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar); $runner->run(); This module is probably incomplete. It is intended to be a wrapper for running java programs..
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License: Freeware | Size: 942.08 KB | Download (96): Bio::Tools::Run::JavaRunner Download |
Bio::Graphics::Glyph::cds module contains the "cds" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the...
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License: Freeware | Size: 4.7 MB | Download (95): Bio::Graphics::Glyph::cds Download |
Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;...
Platforms: *nix
License: Freeware | Size: 5.7 MB | Download (99): Bio::Graphics::Panel 1.5.2_005 Download |
Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. SYNOPSIS use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => transcript, -name => alpha-1...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (100): Bio::Graphics::Feature Download |
Bio::DB::Flat::BDB::swissprot is a swissprot adaptor for Open-bio standard BDB-indexed flat file. SYNOPSIS See Bio::DB::Flat. This module allows swissprot files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (136): Bio::DB::Flat::BDB::swissprot Download |