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Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

Abstract

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here, we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software.

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Authors
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Citation
Category
Journal Paper
Divisions
Bioinformatics and Computational Biology
Journal or Publication Title
Systematic Biology
ISSN
1063-5157
Publisher
Oxford University Press, on behalf of the Society of Systematic Biologists
Place of Publication
London
Page Range
pp. 997-1008
Number
6
Volume
65
Date
November 2016
Official URL
http://dx.doi.org/10.1093/sysbio/syw037
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