Inferring phylogenies of evolving sequences without multiple sequence alignment

Chan, Cheong Xin, Bernard, Guillaume, Poirion, Olivier, Hogan, James M., & Ragan, Mark A. (2014) Inferring phylogenies of evolving sequences without multiple sequence alignment. Scientific Reports, 4, e6504:1-e6504:9.

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Abstract

Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.

Impact and interest:

7 citations in Scopus
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8 citations in Web of Science®

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ID Code: 82330
Item Type: Journal Article
Refereed: Yes
Keywords: Approximate word matches, Maximum-likelihood, Evolution, Gene, Performance, Trees
DOI: 10.1038/srep06504
ISSN: 2045-2322
Divisions: Current > Schools > School of Electrical Engineering & Computer Science
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2014 The Author(s)
Copyright Statement: This work is licensed under a Creative Commons Attribution-NonCommercial-
ShareAlike 4.0 International License.The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated
otherwise in the credit line; if the material is not included under the Creative
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in order to reproduce the material. To view a copy of this license, visit http://
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Deposited On: 09 Mar 2015 23:06
Last Modified: 16 Mar 2015 00:03

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