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This paper presents an algorithm to detect lateral gene transfer (LGT) on the basis of pairwise evolutionary distances. The prediction is made from a likelihood ratio derived from hypotheses of LGT versus no LGT, using multivariate normal theory. In contrast to approaches based on explicit phylogenetic LGT detection, it avoids the high computational cost and pitfalls associated with gene tree inference,...
The OMA project is a large-scale effort to identify groups of orthologs from complete genome data, currently 150 species. The algorithm relies solely on protein sequence information and does not require any human supervision. It has several original features, in particular a verification step that detects paralogs and prevents them from being clustered together. Consistency checks and verification...