DARKHORSE

DarkHorse is a bioinformatic algorithm for rapid, automated identification and ranking of phylogenetically atypical proteins within assembled genomic or metagenomic data sets. It works by selecting taxonomically classified potential ortholog matches from a reference database of amino acid sequences, then using these matches to calculate a lineage probability index (LPI) score for each unknown query protein... LPI scores are inversely proportional to the phylogenetic distance between query sequences and database matches. DarkHorse is configurable for varying degrees of phylogenetic granularity and protein sequence conservation, enabling evaluation of historical ages associated with putative HGT events. Because the program does not require exact matches, it is particularly useful for classifying sequences from novel taxa with only distant database relatives. Users should consult the references cited below for a complete explanation of parameter selection and result interpretation. A..