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Sci Rep. 2014 Sep 30;4:6504. doi: 10.1038/srep06504.

Inferring phylogenies of evolving sequences without multiple sequence alignment.

Author information

1
Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia.
2
1] Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia [2].
3
School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane, QLD 4000, Australia.

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.

PMID:
25266120
PMCID:
PMC4179140
DOI:
10.1038/srep06504
[Indexed for MEDLINE]
Free PMC Article

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