Bio::Phylo - Phylogenetic analysis using perl

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

This is a wrapper around the Beagle library (<>) 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::Gerp - Parses output from GERP

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: 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::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00

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-1.7.2 - 11 Sep 2017 18:12:51 GMT - Search in distribution

Bio::Gonzales::Phylo::Util - utility functions for phylogenetic analysis

JWB/Bio-Gonzales-0.078 - 15 Feb 2018 08:49:11 GMT - Search in distribution

Bio::Phylo::Forest::DBTree - Phylogenetic database as a tree object

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

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::SLR - Wrapper around the SLR program

This is a wrapper around the SLR program. See 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-1.007002 - 15 Sep 2017 04:00:53 GMT - Search in distribution

Bio::PhyloTastic - Perl clients for PhyloTastic

PhyloTastic (<>) 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

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

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 trees for printing

DBAURAIN/Bio-MUST-Core-0.181000 - 10 Apr 2018 22:31:22 GMT - Search in distribution

Tutorial - Hands-on tutorial for using Bio::NEXUS module.

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

The BioPerl distribution from 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::NEXUS::Import - Extends Bio::NEXUS with parsers for file formats of popular phylogeny programs

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

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

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


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

Bio::BioVeL::Service::NeXMLMerger - merges phylogenetic data and metadata into NeXML

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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