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Bio::Graph::SimpleGraph is a Perl module that can create and manipulate undirected graphs. SYNOPSIS use Bio::Graph::SimpleGraph; my $graph=new SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...
Platforms: *nix
License: Freeware | Size: 5.6 MB | Download (107): Bio::Graph::SimpleGraph Download |
Bio::ConnectDots::SimpleGraph is a simple, hopefully fast undirected graph package. SYNOPSIS use SimpleGraph; my $graph=new Bio::ConnectDots::SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...
Platforms: *nix
License: Freeware | Size: 102.4 KB | Download (93): Bio::ConnectDots::SimpleGraph Download |
Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq); $aln = $in->next_aln(); This object can create...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (129): Bio::AlignIO::bl2seq Download |
Bio::AlignIO::msf is a Perl module with msf sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::Align::AlignI objects to and from msf flat file databases. The rest of the documentation details each of...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (96): Bio::AlignIO::msf Download |
Bio::GMOD::Admin::Monitor::blat is a Perl module that can monitor a BLAT server. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $gmod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $gmod->live_version; Update a MOD installation...
Platforms: *nix
License: Freeware | Size: 71.68 KB | Download (106): Bio::GMOD::Admin::Monitor::blat Download |
Bio::Network::IO::dip_tab is a Perl class for parsing interaction data in DIP tab-delimited format. SYNOPSIS Do not use this module directly, use Bio::Network::IO. For example: my $io = Bio::Network::IO->new(-format => dip_tab, -file => data.dip); my $network = $io->next_network; The...
Platforms: *nix
License: Freeware | Size: 99.33 KB | Download (95): Bio::Network::IO::dip_tab Download |
Bio::Phylo::Treedrawer::Svg is a Perl module that creates svg tree drawings. No serviceable parts inside. This module creates a scalable vector graphic from a Bio::Phylo::Trees::Tree object. It is called by the Bio::Phylo::Treedrawer object, so look there to learn how to create tree drawings....
Platforms: *nix
License: Freeware | Size: 102.4 KB | Download (90): Bio::Phylo::Treedrawer::Svg Download |
Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format =>...
Platforms: *nix
License: Freeware | Size: 143.36 KB | Download (97): Bio::Phylo::IO 0.17 Download |
Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new(); This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE)...
Platforms: *nix
License: Freeware | Size: 8.19 KB | Download (110): Bio::SAGE::Comparison Download |
Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data. SYNOPSIS use Bio::SAGE::DataProcessing; $sage = Bio::SAGE::DataProcessing->new(); # open sequence and quality files open( READS, "library.fasta" ); open( QUAL, "library.qual.fasta" ); #...
Platforms: *nix
License: Freeware | Size: 19.46 KB | Download (93): Bio::SAGE::DataProcessing Download |
Bio::ClusterI module is a cluster Perl interface. SYNOPSIS # see the implementations of this interface for details but # basically my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members =...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (87): Bio::ClusterI Download |
Bio::Matrix::PSM::InstanceSite is a PSM site occurance. SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #You can get an InstanceSite object either from a file: my ($instances,$matrix)=$SomePSMFile->parse_next; #or from memory my %params=(seq=>TATAAT, id=>"TATAbox1",...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (115): Bio::Matrix::PSM::InstanceSite Download |
Bio::NEXUS::MatrixBlock is a Perl module that provides functions for handling blocks that have matrices. SYNOPSIS This module is the super class of Characters, Unaligned, and Distances block classes, and indirectly it is a super-class of Data and History blocks, which are both sub-classes of...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (86): Bio::NEXUS::MatrixBlock Download |
Bio::NEXUS::DataBlock is a Perl module that represents the deprecated DATA Block in NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::DataBlock($type, $block, $verbose, $taxlabels_ref); The DataBlock class represents the deprecated Data Block in a NEXUS file. Data Blocks are still used...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (105): Bio::NEXUS::DataBlock Download |
Bio::NEXUS::UnalignedBlock is a Perl module that represents an UNALIGNED block of a NEXUS file. SYNOPSIS if ( $type =~ /unaligned/i ) { $block_object = new Bio::NEXUS::UnalignedBlock($type, $block, $verbose); } This is a class representing an unaligned block in NEXUS file METHODS new...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (91): Bio::NEXUS::UnalignedBlock Download |
Bio::NEXUS::SetsBlock is a Perl module that represents SETS block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::SetsBlock($block_type, $block, $verbose); Parses Sets block of NEXUS file and stores Sets data. METHODS new Title : new Usage : $block_object = new...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (88): Bio::NEXUS::SetsBlock Download |
Bio::GMOD is a unified API for Model Organism Databases. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $mod->live_version; Update a MOD installation use Bio::GMOD::Update;...
Platforms: *nix
License: Freeware | Size: 71.68 KB | Download (103): Bio::GMOD Download |
Bio::NEXUS::DistancesBlock is a Perl module that represents DISTANCES block in NEXUS file. The DistancesBlock class represents a NEXUS Distances Block and provides methods for reading, writing, and accessing data within these blocks. Distances Blocks contain distance matrices, or a table of...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (96): Bio::NEXUS::DistancesBlock Download |
Bio::SeqIO::fastq is a fastq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. This object can transform Bio::Seq and Bio::Seq::SeqWithQuality objects to and from fastq flat file databases. Fastq is a file format used frequently at...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (110): Bio::SeqIO::fastq Download |
VeryDOC HTML Print to Any Converter Command Line product can be used to batch print html, mhtml files or Web URLs to Windows Printer, it is print the whole web page's content to Windows Printer without user interaction, you can use it to full control printer's capability by members of DEVMODE...
Platforms: Windows
License: Shareware | Cost: $79.00 USD | Size: 8.22 MB | Download (307): HTML Print to Any Converter Download |