Search results for "distribution:Bio-Phylo Bio::Tree::Tree"
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::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::Forest::DrawTreeRole - Tree with extra methods for tree drawing
The object models a phylogenetic tree, a container of Bio::Phylo::For- est::Node objects. The tree object inherits from Bio::Phylo::Listable, so look there for more methods. In addition, this subclass of the default tree object Bio::Phylo::Forest::Tr...
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::Generator - Generator of tree topologies
The generator module is used to simulate trees under various models....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Treedrawer - Visualizer of tree shapes
This module prepares a tree object for drawing (calculating coordinates for nodes) and calls the appropriate format-specific drawer....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Forest::Node - Node in a phylogenetic tree
This module has the getters and setters that alter the state of a node object. Useful behaviours (which are also available) are defined in the Bio::Phylo::Forest::NodeRole package....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
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 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::Phylo::Set - Subset of the parts inside a container
Many Bio::Phylo objects are segmented: they contain one or more subparts of the same type. For example, a matrix contains multiple rows; each row contains multiple cells; a tree contains nodes, and so on. Segmented objects all inherit from Bio::Phylo...
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::Forest::DrawNodeRole - Tree node with extra methods for tree drawing
This module defines a node object and its methods. The node is fairly syntactically rich in terms of navigation, and additional getters are provided to further ease navigation from node to node. Typical first daughter -> next sister traversal and rec...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Forest::NodeRole - Extra behaviours for a node in a phylogenetic tree
This module defines a node object and its methods. The node is fairly syntactically rich in terms of navigation, and additional getters are provided to further ease navigation from node to node. Typical first daughter -> next sister traversal and rec...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Parsers::Nhx - Parser used by Bio::Phylo::IO, no serviceable parts inside
This module parses "New Hampshire eXtended" (NHX) tree descriptions in parenthetical format. The node annotations, which are described here: https://sites.google.com/site/cmzmasek/home/software/forester/nhx, are stored as meta annotations in the name...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Listable - List of things, super class for many objects
A listable object is an object that contains multiple smaller objects of the same type. For example: a tree contains nodes, so it's a listable object. This class contains methods that are useful for all listable objects: Matrices (i.e. sets of matrix...
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::PhyloWS - Base class for phylogenetic web services
This is the base class for clients and service that implement the PhyloWS (<http://evoinfo.nescent.org/PhyloWS>) recommendations. This base class isn't used directly, it contains useful methods that are inherited by its children....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Parsers::Tolweb - Parser used by Bio::Phylo::IO, no serviceable parts inside
This module parses Tree of Life data. It is called by the Bio::Phylo::IO facade, don't call it directly. In addition to parsing from files, handles or strings (which are specified by the -file, -handle and -string arguments) this parser can also pars...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC
Bio::Phylo::Taxa::Taxon - Operational taxonomic unit
The taxon object models a single operational taxonomic unit. It is useful for cross-referencing datum objects and tree nodes....
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC