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. 2011 Dec 12;6(12):e28388. doi: 10.1371/journal.pone.0028388

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Halachev et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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By adopting practical accuracy/speed trade-off xBASE-Orth allows for acceptable computational time using reasonable hardware resources and is predicted to be about 15 times faster compared to direct application of OrthoMCL. The vast majority of the computation time is spent performing CDS alignments and operating on the smaller pan-genomes (xBASE-Orth) rather than on the full CDS collection (OrthoMCL) results in significant time advantage. It is more prominent at higher taxonomic levels, where the difference between pan-genome and full CDS collection sizes increases.