gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

TL;DR

gcodeml is a Grid-enabled computational tool that leverages the PAML package to efficiently analyze large phylogenetic datasets for detecting positive selection in biological evolution.

Contribution

This paper introduces gcodeml, a novel Grid-enabled platform that enhances the efficiency of evolutionary analysis using PAML on large datasets.

Findings

Successfully processed large datasets on Grid and clusters

Demonstrated improved computational efficiency

Applicable to other scientific problems

Abstract

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.