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

  1. Chris-Andre Leimeister
  2. Jendrik Schellhorn
  3. Svenja Dörrer
  4. Michael Gerth
  5. Christoph Bleidorn
  6. Burkhard Morgenstern

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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.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giy148

    Chris-Andre Leimeister 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJendrik Schellhorn 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSvenja Schöbel 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Gerth 2Institute for Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB Liverpool, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChristoph Bleidorn 3University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle 2, 37073 Göttingen, Germany4Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), 28006 Madrid, SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBurkhard Morgenstern 1University of Göttingen, Department of Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, Germany5Göttingen Center of Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 GöttingenFind this author on Google ScholarFind this author on PubMedSearch for this author on this site

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy148 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101560 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101561 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101562 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.101563 Reviewer 5: http://dx.doi.org/10.5524/REVIEW.101564

  2. Version published to 10.1093/gigascience/giy148
  3. Version published to 10.1101/306142v3 on bioRxiv
  4. Version published to 10.1101/306142v2 on bioRxiv
  5. Version published to 10.1101/306142v1 on bioRxiv