Search results for "distribution:Bio-Phylo bio::nexus"
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::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::Phylo::NeXML::DOM - XML DOM support for Bio::Phylo
This module adds "to_dom" methods to Bio::Phylo::NeXML::Writable classes, which provide NeXML-valid objects for document object model manipulation. DOM formats currently available are "XML::Twig" and "XML::LibXML". For any "XMLWritable" object, use "...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 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::Phylo::Forest - Container for tree objects
The Bio::Phylo::Forest object models a set of trees. The object subclasses the Bio::Phylo::Listable object, so look there for more methods available to forest objects....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Project - Container for related data
The project module is used to collect taxa blocks, tree blocks and matrices....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Unparsers::Mrp - Serializer used by Bio::Phylo::IO, no serviceable parts inside
This module turns a Bio::Phylo::Forest object into an MRP nexus formatted matrix. It is called by the Bio::Phylo::IO facade, don't call it directly....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Unparsers::Nhx - Serializer used by Bio::Phylo::IO, no serviceable parts inside
This module turns a tree object into a New Hampshire eXtended-formatted (parenthetical) tree description. 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: # by def...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Forest::Tree - Phylogenetic tree
The package has the getters and setters that alter the internal state of a tree object. Additional tree-related behaviours (which are available also) are defined in the package Bio::Phylo::Forest::TreeRole....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Parsers::Figtree - Parser used by Bio::Phylo::IO, no serviceable parts inside
This module parses annotated trees in NEXUS format as interpreted by FigTree (<http://tree.bio.ed.ac.uk/software/figtree/>), i.e. trees where nodes have additional 'hot comments' attached to them in the tree description. The implementation assumes sy...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Unparsers::Figtree - Serializer used by Bio::Phylo::IO, no serviceable parts inside
This module turns objects into a nexus-formatted string that uses additional syntax for Figtree. 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:...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Unparsers::Newick - Serializer used by Bio::Phylo::IO, no serviceable parts inside
This module turns a tree object into a newick formatted (parenthetical) tree description. 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: # by default, names for ...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::NeXML::Writable - Superclass for objects that serialize to NeXML
This is the superclass for all objects that can be serialized to NeXML (<http://www.nexml.org>)....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Util::Exceptions - Errors ($@) that are objects
Sometimes, Bio::Phylo dies. If this happens because you did something that brought Bio::Phylo into an undefined and dangerous state (such as might happen if you provide a non-numerical value for a setter that needs numbers), Bio::Phylo will throw an ...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Forest::TreeRole - Extra behaviours for a phylogenetic tree
The object models a phylogenetic tree, a container of Bio::Phylo::Forest::Node objects. The tree object inherits from Bio::Phylo::Listable, so look there for more methods....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Matrices::MatrixRole - Extra behaviours for a character state matrix
This module defines a container object that holds Bio::Phylo::Matrices::Datum objects. The matrix object inherits from Bio::Phylo::Listable, so the methods defined there apply here....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::PhyloWS::Service::Tolweb - PhyloWS service wrapper for Tree of Life
This is an example implementation of a PhyloWS service. The service wraps around the Tree of Life XML services described at <http://tolweb.org/tree/home.pages/downloadtree.html>. When doing a record lookup this service returns project objects that in...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC