Zmasek CM, Eddy SR
RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.
BMC bioinformatics. 2002-05-16; 3.14.
When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein's function than paralogous sequences (that diverged by gene duplication). The utility of phylogenetic information in high-throughput genome annotation ("phylogenomics") is widely recognized, but existing approaches are either manual or not explicitly based on phylogenetic trees.
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