multiPAML2.5: a Python script to run multiple molecular evolution PAML analyses

PISCIOTTANO, FRANCISCO; CAMPOS, MARÍA CLARA; SARAGÜETA, PATRICIA

Corrientes

Congreso; XII Congreso Argentino de Bioinformática y Biología Computacional; 2022

Asociación Argentina de Bioinformática y Biología Computacional

DN/DS positive selection analyses are a widespread approach to search for signatures of darwinian molecular evolution. Among the available software to perform such analyses the package of programs PAML (Phylogenetic Analysis by Maximum Likelihood) is the most used in order to construct Likelihood Ratio Tests of evolutionary hypotheses. However, testing multiple genes in multiple tree clades/branches involves a set of monotonous and time consuming tasks that can lead to user introduced errors and mistakes.Here we present multiPAML2.5, a simple homemade Python script that was designed to run multiple PAML branch-site positive selection analyses. multiPAML2.5 was designed to help the user deal with the tedious PAML process required to run positive selection tests on multiple genes and/or for multiple branches. The script helps testing multiple evolutionary hypotheses with minimal manual user intervention as ithandles directory organization, files distribution, program execution output file parsing and results gathering of Likelihood Ratio Test.