Orthology prediction at scalable resolution by phylogenetic tree analysis

BMC Bioinformatics

Table 1 Comparing benchmark results for species overlap/species-tree reconciliation

	Species overlap	Species-tree reconciliation
correct	70%	67%
member	7%	4%
ambiguous	4%	3%
related	3%	4%
wrong	16%	22%

Benchmark comparison of the species overlap method with the species tree reconciliation method for orthology prediction. The analysis includes 11624 γ-proteobacteriotic genes from 1006 COGs which have at least 6 genes from the γ-proteobacteria. The species overlap method detects 3391 duplications where the species tree reconciliation method detects 4554. Nevertheless, the species overlap method, which does not assume a species tree, has more orthology assignments that can be considered correct (classes "correct" and "member") than the species tree reconciliation method, and can be considered to be at least on par with it.

ISSN: 1471-2105