| NewickParser | which implements a newick string parser as a finite state
machine which enables it to parse the full Newick specification.
Taken largely from the Ensembl Compara file with the same name
(Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the
parser to work with BioPerl's event handler-based parsing scheme.
This module is used by nhx.pm and newick.pm, and is NOT called
directly. Instead, both of those parsing modules extend this module in
order to gain access to the main parsing method. |
| TreeEventBuilder | Build Bio::Tree::Tree's and
Bio::Tree::Node's from Events |
| cluster | A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output |
| lintree | Parser for lintree output trees |
| newick | Bio::TreeIO::newick |
| nexml | A TreeIO driver module for parsing NeXML tree files |
| nexus | A TreeIO driver module for parsing Nexus tree output from PAUP |
| nhx | TreeIO implementation for parsing
Newick/New Hampshire eXtendend (NHX) format. |
| pag | Bio::TreeIO driver for Pagel format |
| phyloxml | TreeIO implementation for parsing PhyloXML format. |
| svggraph | A simple output format that converts a Tree object to an SVG output |
| tabtree | A simple output format which displays a tree as an ASCII drawing |