dwstree provides a python library for reading and writing newick trees and NEXUS files, manipulating phylogenetic trees, and conducting analysis of phylogenies and traits.
Command-line programs available
All of these modules provide functions/methods and also provide a command-line interface. All of these programs read data in newick (*.new) and/or NEXUS file format. For instructions and a list of options, use the '-h' option when calling the program. For example: type 'python dorder.py -h'.
- icontrasts.py: Calculates independent contrasts. - dorder.py: Provides the Divergence Order Test (DOT) and Synchronized Changes Test (SvS). - branch_lengths.py: Assign branch lengths to a phylogeny according to several different possible algorithms. - cladelabel.py label clades in a phylogeny as defined by a taxa list in an auxilary file.
Use the Python help command or browse the code to understand the phylogenetic tree functions
python setup.py install