PyPHLAWD is an updated version of PHLAWD written in python that has significant improvements and expansions. In addition to baited runs, PyPHLAWD can also do clustering. Specifically, this uses the tip-to-root clustering method as a basis for identifying orthology to assemble large phylogenetic trees. Many of the scripts in PyPHLAWD may be run separately allowing the functions of the program to be performed without requiring the full analysis. You can find several how-tos and tutorials and other information for specific scripts in different parts of the website.


The first use of PyPHLAWD was in

  • Smith, S. A. and J. W. Brown. 2018. Constructing a broadly inclusive seed plant phylogeny. American Journal of Botany 105(3): 1–13. link

The program is described in

  • Smith, S. A. and J. F. Walker. in review. PyPHLAWD: a python package for phylogenetic dataset construction

PyPHLAWD is currently in a rolling release format. You can refer to your current version if you git clone the repository by running the command python logo.py. That will give you the hash for the version you are running as below