PhyloPyPruner: Tree-based Orthology Inference for Phylogenomics with New Methods for Identifying and Excluding Contamination
Motivation: Large-scale phylogenetic analyses rely on orthology inference to curate sets of sequences related by speciation rather than gene duplication. Graph-based ‘orthology’ inference approaches cluster sequences together based on an all-versus-all BLAST, followed by filtering by hit fraction, Markov clustering, or both, but the output of such approaches often contains paralogous sequences. Tr
