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

A2B2C

multiPAML2.5: a Python script to run multiple molecular evolution PAML analysis Francisco Pisciottano, María Clara Campos and Patricia SaragüetaInstituto de Biología y Medicina Experimental - CABA, ArgentinaBACKGROUNDDN/Ds positive selection analysis is a widespread approach to search signatures of molecular evolution and to identify genes involved in evolutionary events. 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.RESULTSHere 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 to deal with the tedious PAML process required to run positive selection tests on multiple genes. The script considerer multiple evolutionary hypotheses with minimal manual user intervention as it handles directory organization, files distribution, program execution, results gathering of Likelihood Ratio Test.multiPAML2.5 were implemented and tested in the evolutionary analysis of gamete interaction proteins along the Carnivora order. Several oocyte (ZP1, ZP2, ZP3, ZP4, IZUMO1R) and sperm (ZP3R, ZAN, SLLP1, PKDREJ, IZUMO1) proteins were analyzed from highly curated MSAs. multiPaml2.5 allowed us to test multiple evolutionary hypotheses of both episodic and divergent positive selection in the basal branch and the sub-trees of Carnivora, Caniformes, Feliformes and Pantherines for the listed genes in just one scrip run, rendering an organized directories hierarchy and a single simple but efficient output results file. CONCLUSIONSmultiPAML2.5 proved to be a handy and accessible way of running numerous PAML analyses from multiple MSAs, sparing the user the trivial chores required to set a PAML analysis and gather results which are error-prone and time-consuming when performed manually.In the example of the gamete interaction proteins of the Carnivora order showed here, the results will be useful to understand the molecular basis of the lack of felid precygotic reproductive isolation comparing to canids, its sister group.