FastCodeML is a software to infer positive selection along positions of a protein coding gene using the Branch-Site model of evolution (Yang and Nielsen, 2002, Mol Biol Evol). Although the model is similar to the one implemented in the codeml software from the PAML package, our goal was to focus on the computational efficiency by developing an improved serial implementation but also provide new parallelisation strategies.
By using an hybrid (OpenMP/MPI) strategy, FastCodeML can reach a speed-up of up to 10 times compared with codeml. The speed-up will increase with larger data sets.
To download, please use the ftp server of the Swiss Institute of Bioinformatics.
For questions, please send an email to selectome [at] unil.ch
Reference
When using this software, please cite:
Valle M., Schabauer H., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Salamin N., 2014. Optimisation strategies for fast detection of positive selection on phylogenetic trees. Bioinformatics 30(8): 1129.1137.