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Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees

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Comparative Genomics (RECOMB-CG 2018)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11183))

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Abstract

Word-based or ‘alignment-free’ methods for phylogeny reconstruction are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free methods calculate pairwise distances for a set of input sequences, for example from word frequencies, from so-called spaced-word matches or from the average length of common substrings. In this paper, we propose the first word-based phylogeny approach that is based on multiple sequence comparison and Maximum Likelihood. Our algorithm first samples small, gap-free alignments involving four taxa each. For each of these alignments, it then calculates a quartet tree and, finally, the program Quartet MaxCut is used to infer a super tree for the full set of input taxa from the calculated quartet trees. Experimental results show that trees calculated with our approach are of high quality.

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Funding

The project was funded by VW Foundation, project VWZN3157. We acknowledge support by the Open Access Publication Funds of Göttingen University.

Author information

Authors and Affiliations

  1. Department of Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany

    Thomas Dencker, Chris-André Leimeister & Burkhard Morgenstern

  2. Institute for Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK

    Michael Gerth

  3. Department of Animal Evolution and Biodiversity, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany

    Christoph Bleidorn

  4. Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), 28006, Madrid, Spain

    Christoph Bleidorn

  5. Institute of Evolution, Department of Evolutionary and Environmental Biology, University of Haifa, 199 Aba Khoushy Ave. Mount Carmel, Haifa, Israel

    Sagi Snir

  6. Goettingen Center of Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany

    Burkhard Morgenstern

Authors
  1. Thomas Dencker
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  2. Chris-André Leimeister
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  3. Michael Gerth
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  4. Christoph Bleidorn
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  5. Sagi Snir
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  6. Burkhard Morgenstern
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Corresponding author

Correspondence to Burkhard Morgenstern .

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Editors and Affiliations

  1. McGill University, Montréal, QC, Canada

    Mathieu Blanchette

  2. Université de Sherbrooke, Sherbrooke, QC, Canada

    Aïda Ouangraoua

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Dencker, T., Leimeister, CA., Gerth, M., Bleidorn, C., Snir, S., Morgenstern, B. (2018). Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees. In: Blanchette, M., Ouangraoua, A. (eds) Comparative Genomics. RECOMB-CG 2018. Lecture Notes in Computer Science(), vol 11183. Springer, Cham. https://doi.org/10.1007/978-3-030-00834-5_13

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  • DOI: https://doi.org/10.1007/978-3-030-00834-5_13

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