Search results for "module:Bio::NEXUS"
Bio::NEXUS - An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format
This is the base class for the Bio::NEXUS package, providing an object-oriented API to the NEXUS file format of *Maddison, et al.*, 1997. This module provides methods to add/remove blocks, select blocks/trees/subtrees/OTUs/characters and so on. For a...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC
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
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
Bio::AlignIO::nexus - NEXUS format sequence input/output stream
This object can transform Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::NEXUS::Util::Logger - Logging for Bio::NEXUS.
This class defines a logger, a utility object for logging messages. The other objects in Bio::NEXUS use this logger to give detailed feedback about what they are doing at per-class, user-configurable log levels (debug, info, warn, error and fatal). Y...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC
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
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
Bio::Phylo::Unparsers::Nexus - Serializer used by Bio::Phylo::IO, no serviceable parts inside
This module turns a Bio::Phylo::Matrices::Matrix object into a nexus formatted matrix. It is called by the Bio::Phylo::IO facade, don't call it directly. You can pass the following additional arguments to the unparse call: # an array reference of mat...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::NEXUS::Util::Exceptions - Exception classes for Bio::NEXUS.
Sometimes, Bio::NEXUS dies. If this happens because you did something that brought Bio::NEXUS into an undefined and dangerous state (such as might happen if you provide a non-numerical value for a setter that needs numbers), Bio::NEXUS will throw an ...
ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC
lib/Bio/BioVeL/Service/NeXMLMerger/CharSetReader/nexus.pm
RVOSA/Bio-BioVeL-0.1
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21 Mar 2014 10:32:41 UTC
lib/Bio/BioVeL/Service/NeXMLMerger/TreeReader/nexus.pm
RVOSA/Bio-BioVeL-0.1
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21 Mar 2014 10:32:41 UTC
lib/Bio/BioVeL/Service/NeXMLMerger/DataReader/nexus.pm
RVOSA/Bio-BioVeL-0.1
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21 Mar 2014 10:32:41 UTC
Bio::TreeIO - Parser for Tree files
This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI objects....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO - Handler for AlignIO Formats
Bio::AlignIO is a handler module for the formats in the AlignIO set, for example, Bio::AlignIO::fasta. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a Bio::Align::AlignI-compliant object. The idea...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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
Bio::PhyloRole - Extra behaviours for the base class
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 UTC
Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format
Convert a Bio::TreeIO to Pagel format. More information here http://www.evolution.reading.ac.uk/index.html...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Phylo::Taxa - Container of taxon objects
The Bio::Phylo::Taxa object models a set of operational taxonomic units. The object subclasses the Bio::Phylo::Listable object, and so the filtering methods of that class are available. A taxa object can link to multiple forest and matrix objects....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC