PyPHLAWD: A python tool for phylogenetic dataset construction

Abstract

Comprehensive phylogenetic trees are essential for many ecological and evolutionary studies. Researchers may use existing trees or construct their own. In order to infer new trees, researchers often rely on programmes that construct datasets from publicly available molecular data.Here, we present PyPHLAWD, a phylogenetically guided tool written in python that creates molecular datasets for building trees. PyPHLAWD constructs clusters (putative orthologs) that may be used for downstream analyses and provides users with a set of easy to interpret results. PyPHLAWD can conduct both baited (analyses that require the identification of gene regions a priori) and clustering analyses (analyses that do not require a priori identification of gene regions).PyPHLAWD is extensible, flexible, open source, and available at https://github.com/FePhyFoFum/PyPHLAWD, with a detailed website outlining instructions and functionality at https://fephyfofum.github.io/PyPHLAWD/.The utility of PyPHLAWD is highlighted here with an example workflow for the plant clade Dipsacales and may be applied to any clade with publicly available data on GenBank.