Two C++ libraries for counting trees on a phylogenetic terrace
| Autor: | Johannes Ernst, Fedor Scholz, Axel Trefzer, Florian Weber, Tobias Ribizel, Peter Bozsoky, Alexandros Stamatakis, Rudolf Biczok, Peter Eisenmann, Michael Hamann |
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| Rok vydání: | 2017 |
| Předmět: |
0106 biological sciences
0301 basic medicine Statistics and Probability Theoretical computer science Phylogenetic inference Phylogenetic tree Computer science DATA processing & computer science Computational Biology Network topology 010603 evolutionary biology 01 natural sciences Biochemistry Applications Notes Computer Science Applications Phylogenetics 03 medical and health sciences Computational Mathematics 030104 developmental biology Computational Theory and Mathematics ddc:004 Molecular Biology Algorithms Phylogeny Software |
| Zdroj: | Bioinformatics Bioinformatics, 34 (19), 3399–3401 |
| ISSN: | 1367-4811 1367-4803 1460-2059 |
| Popis: | Motivation The presence of terraces in phylogenetic tree space, i.e. a potentially large number of distinct tree topologies that have exactly the same analytical likelihood score, was first described by Sanderson et al. 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 lack of an efficient library 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. Results In our bioinformatics practical that is set up as a programming contest we developed two efficient and independent C++ implementations of the SUPERB algorithm by Constantinescu and Sankoff (1995) for counting and enumerating trees on a terrace. Both implementations yield exactly the same results, are more than one order of magnitude faster, and require one order of magnitude less memory than a previous thirrd party python implementation. Availability and implementation The source codes are available under GNU GPL at https://github.com/terraphast. Supplementary information Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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