Search results for "Bio::Matrix::IO"
Bio::Matrix::IO - A factory for Matrix parsing
This is a general factory framework for writing parsers for Matricies. This includes parsing output from distance output like PHYLIP's ProtDist. Additionally it should be possible to fit parsers for PWM and PSSMs once their Matrix objects are written...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Matrix::PSM::IO - PSM parser
- Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix
- Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies
- 18 more results from BioPerl »
Bio::Gonzales::Matrix::IO - Library for simple matrix IO
Provides functions for common matrix/list IO....
JWB/Bio-Gonzales-0.083 - 02 Jan 2021 23:10:48 UTC - Search in distribution- lib/Bio/Gonzales/Matrix/IO/mcl.pm
- lib/Bio/Gonzales/Matrix/IO/csv.pm
- Bio::Gonzales - Speedy functions to manipulate biological data
- 1 more result from Bio-Gonzales »
Bio::NEXUS
This User Manual explains the motivation for developing the Bio::NEXUS library, the principles underlying its organization, and its use in developing software for evolutionary informatics. This manual also provides information on how to use two demon...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC - Search in distribution
Bio::NexmlIO - stream handler for NeXML documents
Bio::NexmlIO is an I/O handler for a NeXML document. A NeXML document can represent three different data types: simple sequences, alignments, and trees. NexmlIO has four main methods next_tree, next_seq, next_aln, and write. NexmlIO returns bioperl s...
CJFIELDS/Bio-NeXMLIO-1.7.3 - 11 Sep 2018 18:47:25 UTC - Search in distribution
Bio::Phylo::IO - Front end for parsers and serializers
The IO module is the front end for parsing and serializing phylogenetic data objects. It is a non-OO module that optionally exports the 'parse' and 'unparse' subroutines into the caller's namespace, using the "use Bio::Phylo::IO qw(parse unparse);" d...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC - Search in distribution- Bio::Phylo::Forest::TreeRole - Extra behaviours for a phylogenetic tree
- Bio::Phylo::Project - Container for related data
- Bio::Phylo::Manual - High-level user guide
- 8 more results from Bio-Phylo »
Bio::Draw::Pictogram - generate SVG output of Pictogram display for consensus motifs
A module for generating SVG output of Pictogram display for consensus motifs. This method of representation was describe by Burge and colleagues: (Burge, C.B.,Tuschl, T., Sharp, P.A. in The RNA world II, 525-560, CSHL press, 1999) This is a simple mo...
CJFIELDS/Bio-Draw-Pictogram-1.7.3 - 25 Sep 2018 01:19:29 UTC - Search in distribution
Bio::Phylo::Beagle - Perl wrapper around BEAGLE
This is a wrapper around the Beagle library (<http://dx.doi.org/10.1093/sysbio/syr100>) that accepts Bio::Phylo objects to simplify data handling....
RVOSA/Bio-Phylo-Beagle-0.03 - 04 Mar 2012 12:39:35 UTC - Search in distribution
Bio::Tools::Run::Phylo::SLR - Wrapper around the SLR program
This is a wrapper around the SLR program. See http://www.ebi.ac.uk/goldman/SLR/ for more information. This module is more about generating the proper ctl file and will run the program in a separate temporary directory to avoid creating temp files all...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution- Bio::Tools::Run::StandAloneBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
- Bio::Tools::Run::Phylo::Phylip::SeqBoot - Wrapper for the phylip program SeqBoot
- Bio::Tools::Run::Phylo::Phylip::Consense - Wrapper for the phylip program Consense
- 2 more results from BioPerl-Run »
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
Note: this DESCRIPTION only documents the (Bio)perl interface to TCoffee. Helping the module find your executable You will need to enable TCoffee to find the t_coffee program. This can be done in (at least) three ways: 1. Make sure the t_coffee execu...
CDRAUG/Bio-Tools-Run-Alignment-TCoffee-1.7.4 - 09 Jul 2018 18:31:30 UTC - Search in distribution
Bio::Graphics::Pictogram - generate SVG output of Pictogram display for consensus motifs
A module for generating SVG output of Pictogram display for consensus motifs. This method of representation was describe by Burge and colleagues: (Burge, C.B.,Tuschl, T., Sharp, P.A. in The RNA world II, 525-560, CSHL press, 1999) This is a simple mo...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution
Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml
This is a wrapper around the codeml program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information. This module is more about generating the properl codem...
CDRAUG/Bio-Tools-Phylo-PAML-1.7.3 - 01 Jul 2018 12:36:38 UTC - Search in distribution
Bio::Community::IO::Driver::biom - Driver to read and write files in the sparse BIOM format
This Bio::Community::IO::Driver::biom driver reads and writes files in the BIOM format version 1.0 described at <http://biom-format.org/documentation/format_versions/biom-1.0.html>. Multiple communities and additional metadata can be recorded in a BI...
FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 UTC - Search in distribution- Bio::Community::IO::FormatGuesser - Determine the format used by a community file