Search results for "dist:BioPerl Bio::TreeIO"
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
Bio::TreeIO::phyloxml - TreeIO implementation for parsing PhyloXML format.
This module handles parsing and writing of phyloXML format....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::TreeIO::NewickParser - newick string parser
This module correctly parses the Newick and NHX formats, sending calls to the BioPerl TreeEventHandler when appropriate in order to build and populate the node objects. Module which implements a newick string parser as a finite state machine which en...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
This object will take events and build a Bio::Tree::TreeI compliant object makde up of Bio::Tree::NodeI objects....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_tree2pag - convert Bio::TreeIO parseable format trees to pagel format
Convert TreeIO parseable files into Pagel format tree files. Be warned that pagel format only really supports a single tree per file so. Also Pagel parsing is not yet available in bioperl....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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::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::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::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::SeqIO::seqxml - SeqXML sequence input/output stream
This object can transform Bio::Seq objects to and from SeqXML format. For more information on the SeqXML standard, visit <http://www.seqxml.org>. In short, SeqXML is a lightweight sequence format that takes advantage of the validation capabilities of...
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::Tools::Phylo::Molphy - parser for Molphy output
A parser for Molphy output (protml,dnaml)...
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