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Compressing Streams of Phylogenetic Trees

Axel Trefzer, View ORCID ProfileAlexandros Stamatakis
doi: https://doi.org/10.1101/440644
Axel Trefzer
*Karlsruhe Institute of Technology, Karslruhe, Germany,
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  • For correspondence: trefaxel@gmail.com
Alexandros Stamatakis
†Heidelberg Institute for Theoretical Studies, Heidelberg, Germany,
*Karlsruhe Institute of Technology, Karslruhe, Germany,
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  • ORCID record for Alexandros Stamatakis
  • For correspondence: Alexandros.Stamatakis@h-its.org trefaxel@gmail.com
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Abstract

Bayesian Markov-Chain Monte Carlo (MCMC) methods for phylogenetic tree inference, that is, inference of the evolutionary history of distinct species using their molecular sequence data, typically generate large sets of phylogenetic trees. The trees generated by the MCMC procedure are samples of the posterior probability distribution that MCMC methods approximate. Thus, they generate a stream of correlated binary trees that need to be stored. Here, we adapt state-of-the art algorithms for binary tree compression to phylogenetic tree data streams and extend them to also store the required meta-data. On a phylogenetic tree stream containing 1, 000 trees with 500 leaves including branch length values, we achieve a compression rate of 5.4 compared to the uncompressed tree files and of 1.8 compared to bzip2-compressed tree files. For compressing the same trees, but without branch length values, our compression method is approximately an order of magnitude better than bzip2. A prototype implementation is available at https://github.com/axeltref/tree-compression.git.

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  • This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 15, 2018.
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Compressing Streams of Phylogenetic Trees
Axel Trefzer, Alexandros Stamatakis
bioRxiv 440644; doi: https://doi.org/10.1101/440644
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Compressing Streams of Phylogenetic Trees
Axel Trefzer, Alexandros Stamatakis
bioRxiv 440644; doi: https://doi.org/10.1101/440644

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