Bio::Phylo - Phylogenetic analysis using perl River stage two • 8 direct dependents • 11 total dependents

This is the base class for the Bio::Phylo package for phylogenetic analysis using object-oriented perl5. In this file, methods are defined that are performed by other objects in the Bio::Phylo release that inherit from this base class (which you norm...

RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 GMT - Search in distribution

Bio::Phylo::Beagle - Perl wrapper around BEAGLE River stage zero No dependents

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 GMT - Search in distribution

Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 River stage one • 1 direct dependent • 1 total dependent

This module is used to parse the output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio::Tools::Run::Phylo::PAML::* modules to actually run some of the PAML programs, but this module is only useful to parse t...

CDRAUG/Bio-Tools-Phylo-PAML-1.7.3 - 01 Jul 2018 12:36:38 GMT - Search in distribution

Bio::Tools::Phylo::Gerp - Parses output from GERP River stage two • 35 direct dependents • 37 total dependents

This module is used to parse the output from 'GERP' (v2) by Eugene Davydov (originally Gregory M. Cooper et al.). You can get details here: http://mendel.stanford.edu/sidowlab/ It works on the .elems files produced by gerpelem. Each result is a Bio::...

CJFIELDS/BioPerl-1.007002 - 11 Sep 2017 21:25:08 GMT - Search in distribution

Bio::Gonzales::Phylo::Util - utility functions for phylogenetic analysis River stage one • 1 direct dependent • 1 total dependent

JWB/Bio-Gonzales-0.082 - 07 Jun 2018 17:48:44 GMT - Search in distribution

Bio::Phylo::Forest::DBTree - Phylogenetic database as a tree object River stage zero No dependents

This package provides the functionality to handle very large phylogenies (examples: the NCBI taxonomy, the Green Genes tree) as if they are Bio::Phylo tree objects, with all the possibilities for traversal, computation, serialization, and visualizati...

RVOSA/Bio-Phylo-Forest-DBTree-v0.1.2 - 24 Oct 2017 14:06:26 GMT - Search in distribution

Bundle::Bio::Phylo::PhyLoTA - Modules used in supersmart-phylota project River stage zero No dependents

Modules used in supersmart-phylota project....

KARINILS/Bundle-Bio-Phylo-PhyLoTA-0.2 - 27 Sep 2012 13:18:41 GMT - Search in distribution

Bio::Tools::Run::Phylo::LVB - Object for using the LVB program to create an array of Bio::Tree objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1. River stage one • 4 direct dependents • 4 total dependents

Wrapper for LVB, which uses a simulated annealing heuristic search to seek parsimonious trees from a nucleotide multiple alignment....

CJFIELDS/BioPerl-Run-1.007002 - 15 Sep 2017 04:00:53 GMT - Search in distribution

Bio::PhyloTastic - Perl clients for PhyloTastic River stage zero No dependents

PhyloTastic (<http://phylotastic.org>) is community effort to develop interoperable tools for pruning and annotating phylogenetic megatrees. This package contributes to that effort by providing simple client access to web services that perform steps ...

RVOSA/Bio-PhyloTastic-0.2 - 11 Jun 2012 18:58:40 GMT - Search in distribution


Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph River stage one • 1 direct dependent • 1 total dependent

This glyph draws a cladogram for any set of species along with their alignment data in relation to the reference species. At high magnification, base pair alignements will be displayed. At lower magnification, a conservation score plot will be drawn....

CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 GMT - Search in distribution

Bio::EasyYang - A tiny interface for Bio::Tools::Run::Phylo::PAML::Yn00 module River stage zero No dependents

This module is a simple function to execute the Yang algorithm easily....

HVALVERDE/Bio-EasyYang-1 - 13 Nov 2012 10:46:20 GMT - Search in distribution

format-tree.pl - Format trees for printing River stage one • 3 direct dependents • 3 total dependents

DBAURAIN/Bio-MUST-Core-0.182420 - 30 Aug 2018 13:48:54 GMT - Search in distribution

Tutorial - Hands-on tutorial for using Bio::NEXUS module. River stage one • 1 direct dependent • 1 total dependent

Tutorial to get started using Bio::NEXUS module. INTRODUCTION The NEXUS file format standard of Maddison, et al. (1997) is designed to represent sets of data, including character data (e.g., molecular sequence alignments, morphological character sets...

ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 GMT - Search in distribution

Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2 River stage zero No dependents

The BioPerl distribution from http://bioperl.org contains code and modules that may use or require additional 'external' perl modules for advanced functionality. Many of the external modules are not contained within the standard Perl distribution. Th...

CJFIELDS/Bundle-BioPerl-2.1.9 - 16 Jan 2015 20:05:40 GMT - Search in distribution

Bio::NexmlIO - stream handler for NeXML documents River stage zero No dependents

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 GMT - Search in distribution

Bio::NEXUS::Import - Extends Bio::NEXUS with parsers for file formats of popular phylogeny programs River stage zero No dependents

A module that extends Bio::NEXUS with parsers for file formats of popular phylogeny programs....

LIMAONE/Bio-NEXUS-Import-v0.2.0 - 03 Feb 2011 16:30:11 GMT - Search in distribution

FAST::Bio::SeqIO::nexml - NeXML sequence input/output stream River stage zero No dependents

This object can transform FAST::Bio::Seq objects to and from NeXML format. For more information on the NeXML standard, visit <http://www.nexml.org>....

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 GMT - Search in distribution

lib/Bio/Emboss/Methods.pm River stage zero No dependents

PERNST/Bio-Emboss-5.0.0.1 - 06 Sep 2007 16:28:46 GMT - Search in distribution

Bio::BioVeL::Service::NeXMLMerger - merges phylogenetic data and metadata into NeXML River stage zero No dependents

This package merges phylogenetic data and metadata to produce a NeXML document. Although it can be used inside scripts that receive command line arguments, it is intended to be used as a RESTful web service that clients can be written against, e.g. i...

RVOSA/Bio-BioVeL-0.1 - 21 Mar 2014 10:32:41 GMT - Search in distribution

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