PhyloTreePruner

Phylogenomics, phylogenetic inference using large multigene datasets, relies on accurate identification of orthologous sequences among the taxa of interest. In order to improve orthology determination for phylogenomics using a tree-based approach, we have developed PhyloTreePruner, a utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods. Single-gene trees are generated using the user’s preferred method. These trees are then provided to PhyloTreePruner which checks them for evidence of paralogy (i.e., multiple sequences from the same taxon that do not form a clade), trims suspected paralogs from the data matrix, and generates a new alignment containing only sequences inferred as orthologs. Preliminary tests of PhyloTreePruner on a variety of datasets indicate that this method successfully removes paralogous sequences and thus should help improve the accuracy of inferred species trees.