Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences

Word-based or ‘alignment-free’ sequence comparison has become an active area of research in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches isFiltered Spaced Word Matches. Herein, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is calledProt-SpaM. We compare the performance ofProt-SpaMto other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa.Prot-SpaMcan be used to calculate high-quality phylogenetic trees from whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available throughGithub:

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