awitney / pyjar

A python implementation of the joint ancestral state reconstruction algorithm of Pupko et al

pyjar

A python implementation of the joint ancestral state reconstruction algorithm of Pupko et al

Contents

• Requirements
• Usage
• Citation
• License

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.