gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution
Distributed, Parallel, and Cluster Computing
2012-03-15 v1 Computational Engineering, Finance, and Science
Populations and Evolution
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.
Cite
@article{arxiv.1203.3092,
title = {gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution},
author = {Sébastien Moretti and Riccardo Murri and Sergio Maffioletti and Arnold Kuzniar and Briséïs Castella and Nicolas Salamin and Marc Robinson-Rechavi and Heinz Stockinger},
journal= {arXiv preprint arXiv:1203.3092},
year = {2012}
}
Comments
10 pages, 4 figures. To appear in the HealthGrid 2012 conf