Leimeister, Chris-Andre, Schellhorn, Jendrik, Doerrer, Svenja, Gerth, Michael 
ORCID: 0000-0001-7553-4072, Bleidorn, Christoph and Morgenstern, Burkhard
(2019)
<i>Prot-SpaM</i>: fast alignment-free phylogeny reconstruction based on whole-proteome sequences.
GIGASCIENCE, 8 (3).
giy148-.
Abstract
Word-based or 'alignment-free' sequence comparison has become an active research area 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 is Filtered Spaced Word Matches. Here, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM. We compare the performance of Prot-SpaM to other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa. Prot-SpaM can be used to calculate high-quality phylogenetic trees for dozens of 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 through Github: https://github.com/jschellh/ProtSpaM.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | alignment-free, phylogeny, spaced words, micro-alignment, proteome, protein comparison, distance method, Kimura, Wolbachia, amino-acid substitutions |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 24 May 2019 15:34 |
| Last Modified: | 09 Oct 2023 16:55 |
| DOI: | 10.1093/gigascience/giy148 |
| Open Access URL: | https://doi.org/10.1093/gigascience/giy148 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3042816 |
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