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bioRxiv · 10.1101/211276

Two C++ Libraries for Counting Trees on a Phylogenetic Terrace

Biczok, R.·Bozsoky, P.·Eisenmann, P.·Ernst, J.·Ribizel, T.·Scholz, F.·Trefzer, A.·Weber, F.·Hamann, M.·Stamatakis, A.
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Abstract

MotivationThe presence of terraces in phylogenetic tree space, that is, a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al, (2011). However, popular software tools for maximum likelihood and Bayesian phylogenetic inference do not yet routinely report, if inferred phylogenies reside on a terrace, or not. We believe, this is due to the unavailability of an efficient library implementation to (i) determine if a tree resides on a terrace, (ii) calculate how many trees reside on a terrace, and (iii) enumerate all trees on a terrace.\n\nResultsIn our bioinformatics programming practical we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating the trees on a terrace. Both implementations yield exactly the same results and are more than one order of magnitude faster and require one order of magnitude less memory than a previous 3rd party python implementation.\n\nAvailabilityThe source codes are available under GNU GPL at https://github.com/terraphast\n\nContactAlexandros.Stamatakis@h-its.org

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Biczok, R., Bozsoky, P., Eisenmann, P., Ernst, J., Ribizel, T., Scholz, F., Trefzer, A., Weber, F., Hamann, M., Stamatakis, A.. 2017-11-02. Two C++ Libraries for Counting Trees on a Phylogenetic Terrace. https://doi.org/10.1101/211276

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