pyjar
A python implementation of the joint ancestral state reconstruction algorithm of Pupko et al
Contents
Requirements
pyjar requires python3 and the following modules: Bio, dendropy, numpy, scipy.
Usage
usage: usage: pyjar.py [options]
-h, --help show this help message and exit
-a FILE, --alignment FILE
Input alignment file. Required.
-i FILE, --info FILE Input RAxML info file. Optional. By default a JC model
will be applied.
-t FILE, --tree FILE Input tree file. Required.
-o PREFIX, --output_prefix PREFIX
Output prefix. Required.
-v, --verbose More verbose output
Citation
For the joint ancestral reconstruction method, please cite "Tal Pupko, Itsik Pe, Ron Shamir, Dan Graur; A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences, Molecular Biology and Evolution, Volume 17, Issue 6, 1 June 2000, Pages 890-896
License
pyjar is free software, licensed under GPLv3.