Link Your Sites (LYS.py): Coupling your PAML codeml results and homologous protein structures in PyMOL

The visualization of the molecular context of an amino acid mutation in a protein structure is crucial for the assessment of its functional impact and to understand its evolutionary implications. Currently, searches for fast evolving amino acid positions using codon substitution models like those implemented in PAML (Z. Yang, 2000) are done in almost complete proteomes, generating large numbers of candidate proteins that require individual structural analyses. Here I present a python wrapper script that integrates the output of PAML with the PyMOL visualization tool to automate the generation of protein structure models where positively selected sites are mapped along with the location of putative functional domains.