Title:

Improving Phylogenetic Input Data with Phylogenetic Focusing

The growing availability of animal protein sequence data has substantially improved phylogenetic assessments of gene family evolution. However, what sequence data is included when constructing a phylogeny greatly impacts the final result, and the exclusion of informative sequences can lead to incorrect conclusions about tree topography, gene loss or gain events, and gene family evolution. To address the risks of data exclusion, we developed a program called Phylogenetic Focusing. PhyFocus reduces these risks by first conducting a highly permissive search of species’ proteomic data using user-provided query sequences from multiple gene families, then constructing a gene tree for each species. Each species’ gene tree is next “focused” by extracting the subtree representing the gene family of interest. Finally, the subtree sequences are concatenated, filtered for quality via HMMR and alignment editing, and used to construct the final gene family phylogeny. The PhyFocus approach can thus help improve phylogenetic assessments of gene family evolution, and is being developed as a publicly available package.

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