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Bio-Phylo-0.13
River stage two • 9 direct dependents • 18 total dependents
8 ++

Changes for version 0.13

  • Nexus parser now parses interleaved matrices Dependency on Scalar::Util's newness is lessened (i.e. dependency fix, should install easier) Installation choice between MB and EUMM makefiles

Documentation

dndtag.pl
applies unique node labels to newick trees.
Bio::Phylo::Manual
Bio::Phylo v.0.13 user guide.

Modules

Bio::Phylo
Phylogenetic analysis using perl.
Bio::Phylo::Forest
The forest object, a set of phylogenetic trees.
Bio::Phylo::Forest::Node
The tree node object.
Bio::Phylo::Forest::Tree
The tree object.
Bio::Phylo::Generator
Generates random trees.
Bio::Phylo::IO
Input and output of phylogenetic data.
Bio::Phylo::Listable
Parent class for listable/iterator objects.
Bio::Phylo::Matrices
Holds a set of matrix objects.
Bio::Phylo::Matrices::Datum
The single observations object.
Bio::Phylo::Matrices::Matrix
Character state matrix, implements Bio::CDAT::CharMatrixI
Bio::Phylo::Parsers::Newick
Parses newick trees. No serviceable parts inside.
Bio::Phylo::Parsers::Nexus
Parses nexus files. No serviceable parts inside.
Bio::Phylo::Parsers::Table
Parses tab- (or otherwise) delimited matrices. No serviceable parts inside.
Bio::Phylo::Parsers::Taxlist
Parses lists of taxon names. No serviceable parts inside.
Bio::Phylo::Taxa
An object-oriented module for managing taxa.
Bio::Phylo::Taxa::Taxon
The operational taxonomic unit.
Bio::Phylo::Treedrawer
An object-oriented facade for drawing trees.
Bio::Phylo::Treedrawer::Svg
Creates svg tree drawings. No serviceable parts inside.
Bio::Phylo::Unparsers::Mrp
Unparses a forest object into an MRP matrix. No serviceable parts inside.
Bio::Phylo::Unparsers::Newick
Unparses newick trees. No serviceable parts inside.
Bio::Phylo::Unparsers::Nexus
Unparses nexus matrices. No serviceable parts inside.
Bio::Phylo::Unparsers::Pagel
Unparses pagel data files. No serviceable parts inside.
Bio::Phylo::Util::CONSTANT
This package defines global constants and utility functions that operate on them.
Bio::Phylo::Util::Exceptions
Exception classes for Bio::Phylo. No serviceable parts inside.
Bio::Phylo::Util::IDPool
Utility class for generating object IDs

Provides

Bio::Phylo::Deprecated
in lib/Bio/Phylo.pm
Bio::Phylo::Matrices::Alignment
in lib/Bio/Phylo.pm
Bio::Phylo::Matrices::Sequence
in lib/Bio/Phylo.pm
Bio::Phylo::Parsers
in lib/Bio/Phylo.pm
Bio::Phylo::Parsers::Fastnewick
in lib/Bio/Phylo.pm
Bio::Phylo::Parsers::Fastnexus
in lib/Bio/Phylo.pm
Bio::Phylo::Unparsers
in lib/Bio/Phylo.pm

Other files