dwstree provides a python library for reading and writing newick trees and NEXUS files, manipulating phylogenetic trees, and conducting analysis of phylogenies and traits
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dwstree
examples
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README.md
setup.py

README.md

dwstree

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.

Library functions

Use the Python help command or browse the code to understand the phylogenetic tree functions

Installation

python setup.py install