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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 = $cluster->get_members(); my @sub_members =...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (87): Bio::ClusterI Download |
Openwall Linux kernel patch is a collection of security-related features for the Linux kernel, all configurable via the new Security options configuration section. In addition to the new features, some versions of the patch contain various security fixes. The number of such fixes changes from...
Platforms: *nix
License: Freeware | Size: 34.82 KB | Download (94): Openwall Linux kernel patch Download |
Bio::Matrix::PSM::InstanceSite is a PSM site occurance. SYNOPSIS use Bio::Matrix::PSM::InstanceSite; #You can get an InstanceSite object either from a file: my ($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::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...
Platforms: *nix
License: Freeware | Size: 174.08 KB | Download (109): Bio::MCPrimers Download |
OpenSSH SecurID is a patch that integrates SecurID authentication services directly into the OpenSSH daemon. It allows users to use SecurID tokens directly as their passwords instead of relying on the clunky sdshell. This is how it works: 0) apply patch ;-) You must use GNU patch (get it from...
Platforms: *nix
License: Freeware | Size: 48.13 KB | Download (146): OpenSSH SecurID patch Download |
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 (133): Bio::NEXUS::CodonsBlock 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::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 (91): Bio::NEXUS::Functions Download |
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 (90): Bio::NEXUS::NotesBlock 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 |
Unified Qmail Patch provides a concatenation of various patches. Unified Qmail Patch is a concatenation of various patches for the qmail MTA. It supports SMTP AUTH after STARTTLS, Maildir++, regexp support in badmailfrom, and lots of features for high-end production servers.. SourceForge...
Platforms: *nix
License: Freeware | Size: 163.84 KB | Download (103): Unified Qmail Patch Download |