BranchClust is an algorithm for the automated selection of orthologous genes that recognizes orthologous genes from different species in a phylogenetic tree for any number of taxa. The algorithm is capable of distinguishing complete (containing all taxa) and incomplete (not containing all taxa) families and recognizes in- and out-paralogs.
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Maria S Poptsova and J Peter Gogarten
BranchClust: a phylogenetic algorithm for selecting gene families
BMC Bioinformatics 2007, 8:120