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Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

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... Full description

Journal Title: Systematic Biology 2016-11-01, Vol.65 (6), p.997-1008
Main Author: Chernomor, Olga
Other Authors: von Haeseler, Arndt , Minh, Bui Quang
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/27121966
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recordid: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5066062
title: Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
format: Article
creator:
  • Chernomor, Olga
  • von Haeseler, Arndt
  • Minh, Bui Quang
subjects:
  • Algorithms
  • Bioinformatics
  • Biological Evolution
  • Classification - methods
  • Data models
  • Evolution
  • Genomics
  • Inference
  • Matrix
  • Maximum likelihood
  • Missing data
  • Models, Biological
  • partial terraces
  • partition models
  • phylogenetic terraces
  • Phylogenetics
  • phylogenomic inference
  • Phylogeny
  • Regular
  • Regular Articles
  • Sequence Analysis, DNA
  • Software
  • Taxa
  • Topology
ispartof: Systematic Biology, 2016-11-01, Vol.65 (6), p.997-1008
description: 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 data structure for the efficient analysis under partition models. In the presence of missing data exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of 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.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionIn 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 data structure for the efficient analysis under partition models. In the presence of missing data exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of 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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subjectAlgorithms ; Bioinformatics ; Biological Evolution ; Classification - methods ; Data models ; Evolution ; Genomics ; Inference ; Matrix ; Maximum likelihood ; Missing data ; Models, Biological ; partial terraces ; partition models ; phylogenetic terraces ; Phylogenetics ; phylogenomic inference ; Phylogeny ; Regular ; Regular Articles ; Sequence Analysis, DNA ; Software ; Taxa ; Topology
ispartofSystematic Biology, 2016-11-01, Vol.65 (6), p.997-1008
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0Copyright © 2016 Society of Systematic Biologists
1The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. 2016
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abstractIn 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 data structure for the efficient analysis under partition models. In the presence of missing data exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of 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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