Search results for "bio::nexus"
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::NEXUS - An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format
- Bio::NEXUS::Node - Provides functions for manipulating nodes in trees
- Bio::NEXUS::Tree - Provides functions for manipulating trees
- 38 more results from Bio-NEXUS »
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 UTC - Search in distribution- phylip2nex.pl - convert a PHYLIP file into NEXUS format
Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP
This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees. Comments The nexus format allows node comments that are placed inside square brackets. Usually the comments (implemented as tags for nodes) are u...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::AlignIO::nexus - NEXUS format sequence input/output stream
- bp_nexus2nh - convert nexus format trees (from PAUP* and MrBayes) to new hampshire
- Bio::AlignIO - Handler for AlignIO Formats
- 8 more results from BioPerl »
FAST::Bio::AlignIO::nexus - NEXUS format sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::UnivAln - Bioperl alignment object
- FAST::Bio::Align::AlignI - An interface for describing sequence alignments.
- FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
- 3 more results from FAST »
Bio::Phylo::Parsers::Nexus - Parser used by Bio::Phylo::IO, no serviceable parts inside
This module parses nexus files. It is called by the Bio::Phylo::IO module, there is no direct usage. The parser can handle files and strings with multiple tree, taxon, and characters blocks whose links are defined using Mesquite's "TITLE = 'some_name...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC - Search in distribution- Bio::Phylo::Unparsers::Nexus - Serializer used by Bio::Phylo::IO, no serviceable parts inside
- Bio::PhyloRole - Extra behaviours for the base class
- Bio::Phylo::NeXML::Writable - Superclass for objects that serialize to NeXML
- 19 more results from Bio-Phylo »
lib/Bio/BioVeL/Service/NeXMLMerger/CharSetReader/nexus.pm
RVOSA/Bio-BioVeL-0.1
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21 Mar 2014 10:32:41 UTC
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- lib/Bio/BioVeL/Service/NeXMLMerger/TreeReader/nexus.pm
- lib/Bio/BioVeL/Service/NeXMLMerger/DataReader/nexus.pm
- Bio::BioVeL::Service::NeXMLExtractor - extracts and converts data from a NeXML document
- 2 more results from Bio-BioVeL »
lib/Bio/Emboss/Methods.pm
PERNST/Bio-Emboss-5.0.0.1
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06 Sep 2007 16:28:46 UTC
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aln2aln - convert different alignment formats to another alignment format
Takes <input_alignment_file> and converts it to <file_in_other_format> On default, it assumes 'fasta' as input format, but you can use the --from option to make sure that aln2aln uses a different format. Same applies to --to Some formats have a limit...
JWB/Bio-Gonzales-0.083 - 02 Jan 2021 23:10:48 UTC - Search in distribution
format-tree.pl - Format (and annotate) trees for printing
DBAURAIN/Bio-MUST-Core-0.240390
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08 Feb 2024 21:02:36 UTC
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Prospect::Align - Package for overlaying multiple Prospect alignments
Prospect::Align represents an alignment of one or more Prospect structural alignments....
REECE/Prospect-0.92 - 14 Nov 2003 13:16:46 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::Phylo::Hyphy::BatchFile - Wrapper for custom execution of Hyphy batch files
Bio::PhyloTastic - Perl clients for PhyloTastic
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 UTC - Search in distribution- Bio::PhyloTastic::TNRS - Taxonomic Name Reconciliation Service
- Bio::PhyloTastic::PhyleMerge - Merges contents of phylogenetic data files
- Bio::PhyloTastic::TaxTractor - Extracts taxa from phylogenetic file formats
- 3 more results from Bio-PhyloTastic »
Bio::Prospect::Align - Package for overlaying multiple Prospect alignments
Bio::Prospect::Align represents an alignment of one or more Prospect structural alignments....
REECE/Bio-Prospect-1.04 - 19 Nov 2003 06:34:27 UTC - Search in distribution