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Harvey Danger Bio software
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Harvey Danger Bio

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Added: March 24, 2010 | Visits: 960

Bio::Phylo::Manual Bio::Phylo::Manual is a Perl module that contains a Bio::Phylo v.0.14 user guide. This is the manual for Bio::Phylo. Bio::Phylo is a perl5 package for phylogenetic analysis. For installation instructions, read the README file in the root directory of the distribution. The stable URL for the...



Platforms: *nix

License: Freeware Size: 102.4 KB Download (99): Bio::Phylo::Manual Download

Added: August 25, 2010 | Visits: 1.092

Bio::Phylo::Treedrawer::Svg 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 (89): Bio::Phylo::Treedrawer::Svg Download

Added: June 19, 2010 | Visits: 696

Bio::Phylo::IO 0.17 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 (91): Bio::Phylo::IO 0.17 Download

Added: May 09, 2010 | Visits: 1.119

Bio::SAGE::Comparison 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 (104): Bio::SAGE::Comparison Download

Added: June 16, 2010 | Visits: 988

Bio::SAGE::DataProcessing 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 (92): Bio::SAGE::DataProcessing Download

Added: October 06, 2010 | Visits: 673

Bio::ClusterI 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

Added: March 14, 2010 | Visits: 994

Bio::Matrix::PSM::InstanceSite 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 (109): Bio::Matrix::PSM::InstanceSite Download

Added: July 22, 2010 | Visits: 1.176

Bio::MCPrimers Bio::MCPrimers is a Perl module to create molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller. XPORT SUBROUTINES sub find_mc_primers...


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License: Freeware Size: 174.08 KB Download (103): Bio::MCPrimers Download

Added: November 23, 2010 | Visits: 884

Bio::NEXUS::CodonsBlock Bio::NEXUS::CodonsBlock is a Perl module that represents CODONS block in NEXUS file. METHODS new Title : new Usage : block_object = new Bio::NEXUS::CodonsBlock(); Function: Creates a new Bio::NEXUS::CodonsBlock object Returns : Bio::NEXUS::CodonsBlock object Args :.


Platforms: *nix

License: Freeware Size: 153.6 KB Download (127): Bio::NEXUS::CodonsBlock Download

Added: February 09, 2010 | Visits: 797

Bio::NEXUS::MatrixBlock 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

Added: February 24, 2010 | Visits: 843

Bio::NEXUS::DataBlock 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...


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License: Freeware Size: 153.6 KB Download (104): Bio::NEXUS::DataBlock Download

Added: October 22, 2010 | Visits: 838

Bio::NEXUS::UnalignedBlock 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...


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License: Freeware Size: 153.6 KB Download (85): Bio::NEXUS::UnalignedBlock Download

Added: April 10, 2010 | Visits: 706

Bio::NEXUS::SetsBlock 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...


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License: Freeware Size: 153.6 KB Download (87): Bio::NEXUS::SetsBlock Download

Added: September 17, 2010 | Visits: 842

Bio::NEXUS::Functions Bio::NEXUS::Functions is a Perl module that provides private utility functions for the module. This package provides private functions that are not object-specific..


Platforms: *nix

License: Freeware Size: 153.6 KB Download (90): Bio::NEXUS::Functions Download

Added: October 15, 2010 | Visits: 845

Bio::NEXUS::NotesBlock Bio::NEXUS::NotesBlock is a Perl module that represents a NOTES block in a NEXUS file. Placeholding module for the Notes Block class..


Platforms: *nix

License: Freeware Size: 153.6 KB Download (89): Bio::NEXUS::NotesBlock Download

Added: August 25, 2010 | Visits: 948

Bio::GMOD 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;...


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License: Freeware Size: 71.68 KB Download (97): Bio::GMOD Download

Added: July 08, 2010 | Visits: 900

Bio::NEXUS::DistancesBlock 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 (90): Bio::NEXUS::DistancesBlock Download

Added: June 10, 2010 | Visits: 1.279

Bio::SeqIO::fastq 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 (104): Bio::SeqIO::fastq Download

Added: March 16, 2010 | Visits: 594

Bio::ExtractNE::MakeDict Bio::ExtractNE::MakeDict is a package for creating dictionary. FUNCTIONS mkdict($input_file, $output_dictfile) This function creates named-entity dictionary. Note that $input_file is a hash. Currently, only SwissProt data is supported. mkdict({ sprot_file => "sprot", } => "sprot.dict");...


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License: Freeware Size: 5.3 MB Download (117): Bio::ExtractNE::MakeDict Download

Released: September 17, 2012  |  Added: September 17, 2012 | Visits: 505

Bio-Formats Bio-Formats was specially designed as an accessible Java-based tool that can be used for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.


Platforms: Windows

License: Freeware Download (48): Bio-Formats Download

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