Search results for "dist:BioPerl Bio::Tree::Tree"
Bio::Tree::Tree - An implementation of the TreeI interface.
This object holds handles to Nodes which make up a tree....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::Node - A Simple Tree Node
Makes a Tree Node suitable for building a Tree....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::NodeI - Interface describing a Tree Node
A NodeI is capable of the basic structure of building a tree and storing the branch length between nodes. The branch length is the length of the branch between the node and its ancestor, thus a root node in a Tree will not typically have a valid bran...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
This object holds a pointer to the Root of a Tree which is a Bio::Tree::NodeI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
Makes a Tree Node with NHX tags, suitable for building a Tree. See Bio::Tree::Node for a full list of functionality....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::Compatible - Testing compatibility of phylogenetic trees with nested taxa.
NB: This module has exclusively class methods that work on Bio::Tree::TreeI objects. An instance of Bio::Tree::Compatible cannot itself represent a tree, and so typically there is no need to create one. Bio::Tree::Compatible is a Perl tool for testin...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object
Provides a Bio::AnnotationI object which contains a Bio::Tree::TreeI, which can be added to a Bio::AnnotationCollectionI, which in turn be attached to a Bio::AnnotatableI (typically a Bio::AlignI object)...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::Statistics - Calculate certain statistics for a Tree
This should be where Tree statistics are calculated. It was previously where statistics from a Coalescent simulation. It now contains several methods for calculating Tree-Trait statistics....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::RandomFactory - TreeFactory for generating Random Trees
Builds a random tree every time next_tree is called or up to -maxcount times. This module was originally written for Coalescent simulations see Bio::PopGen::Simulation::Coalescent. I've left the next_tree method intact although it is not generating r...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods
This interface provides a set of implemented Tree functions which only use the defined methods in the TreeI or NodeI interface....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::DistanceFactory - Construct a tree using distance based methods
This is a factory which will construct a phylogenetic tree based on the pairwise sequence distances for a set of sequences. Currently UPGMA (Sokal and Michener 1958) and NJ (Saitou and Nei 1987) tree construction methods are implemented....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::AnnotatableNode - A Tree Node with support for annotation
Makes a Tree Node with Annotations, suitable for building a Tree. See Bio::Tree::Node for a full list of functionality....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 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::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::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 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::TreeIO::newick - parsing and writing of Newick/PHYLIP/New Hampshire format
This module handles parsing and writing of Newick/PHYLIP/New Hampshire format....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing
This is a made up format just for outputting trees as an ASCII drawing....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::TreeIO::lintree - Parser for lintree output trees
Parser for the lintree output which looks like this 13 sequences 1000 bootstraping 1 A-salina 2 C-vittat 3 C-sp. 4 L-aequit 5 P-camtsc 6 E-tenuim 7 L-splend 8 P-bernha 9 P-acadia 10 P-p(NE) 11 P-p(GU) 12 P-l(NE) 13 P-l(GU) 14 and 2 0.098857 1000 14 a...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
This is a driver module for parsing Algorithm::Cluster::treecluster() output....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC