Inferring phylogenies of evolving sequences without multiple sequence alignment
Identifieur interne : 001E54 ( Ncbi/Checkpoint ); précédent : 001E53; suivant : 001E55Inferring phylogenies of evolving sequences without multiple sequence alignment
Auteurs : Cheong Xin Chan [Australie] ; Guillaume Bernard [Australie] ; Olivier Poirion [Australie, France] ; James M. Hogan [Australie] ; Mark A. Ragan [Australie]Source :
- Scientific Reports [ 2045-2322 ] ; 2014.
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
Url:
DOI: 10.1038/srep06504
PubMed: 25266120
PubMed Central: 4179140
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Inferring phylogenies of evolving sequences without multiple sequence alignment</title><author><name sortKey="Chan, Cheong Xin" sort="Chan, Cheong Xin" uniqKey="Chan C" first="Cheong Xin" last="Chan">Cheong Xin Chan</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Bernard, Guillaume" sort="Bernard, Guillaume" uniqKey="Bernard G" first="Guillaume" last="Bernard">Guillaume Bernard</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Poirion, Olivier" sort="Poirion, Olivier" uniqKey="Poirion O" first="Olivier" last="Poirion">Olivier Poirion</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="a3">Current address: Laboratoire Ampère, CNRS UMR 5005, École Centrale de Lyon, France.</nlm:aff><country xml:lang="fr" wicri:curation="lc">France</country><wicri:regionArea>Current address: Laboratoire Ampère, CNRS UMR 5005, École Centrale de Lyon</wicri:regionArea><wicri:noRegion>École Centrale de Lyon</wicri:noRegion><wicri:noRegion>École Centrale de Lyon</wicri:noRegion></affiliation></author><author><name sortKey="Hogan, James M" sort="Hogan, James M" uniqKey="Hogan J" first="James M." last="Hogan">James M. Hogan</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>School of Electrical Engineering and Computer Science, Queensland University of Technology</institution>, Brisbane, QLD 4000, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4000</wicri:regionArea><wicri:noRegion>QLD 4000</wicri:noRegion></affiliation></author><author><name sortKey="Ragan, Mark A" sort="Ragan, Mark A" uniqKey="Ragan M" first="Mark A." last="Ragan">Mark A. Ragan</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25266120</idno><idno type="pmc">4179140</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4179140</idno><idno type="RBID">PMC:4179140</idno><idno type="doi">10.1038/srep06504</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000128</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000128</idno><idno type="wicri:Area/Pmc/Curation">000128</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000128</idno><idno type="wicri:Area/Pmc/Checkpoint">001515</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001515</idno><idno type="wicri:Area/Ncbi/Merge">001E54</idno><idno type="wicri:Area/Ncbi/Curation">001E54</idno><idno type="wicri:Area/Ncbi/Checkpoint">001E54</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Inferring phylogenies of evolving sequences without multiple sequence alignment</title><author><name sortKey="Chan, Cheong Xin" sort="Chan, Cheong Xin" uniqKey="Chan C" first="Cheong Xin" last="Chan">Cheong Xin Chan</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Bernard, Guillaume" sort="Bernard, Guillaume" uniqKey="Bernard G" first="Guillaume" last="Bernard">Guillaume Bernard</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author><author><name sortKey="Poirion, Olivier" sort="Poirion, Olivier" uniqKey="Poirion O" first="Olivier" last="Poirion">Olivier Poirion</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="a3">Current address: Laboratoire Ampère, CNRS UMR 5005, École Centrale de Lyon, France.</nlm:aff><country xml:lang="fr" wicri:curation="lc">France</country><wicri:regionArea>Current address: Laboratoire Ampère, CNRS UMR 5005, École Centrale de Lyon</wicri:regionArea><wicri:noRegion>École Centrale de Lyon</wicri:noRegion><wicri:noRegion>École Centrale de Lyon</wicri:noRegion></affiliation></author><author><name sortKey="Hogan, James M" sort="Hogan, James M" uniqKey="Hogan J" first="James M." last="Hogan">James M. Hogan</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>School of Electrical Engineering and Computer Science, Queensland University of Technology</institution>, Brisbane, QLD 4000, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4000</wicri:regionArea><wicri:noRegion>QLD 4000</wicri:noRegion></affiliation></author><author><name sortKey="Ragan, Mark A" sort="Ragan, Mark A" uniqKey="Ragan M" first="Mark A." last="Ragan">Mark A. Ragan</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, The University of Queensland</institution>, Brisbane, QLD 4072, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>, Brisbane, QLD 4072</wicri:regionArea><wicri:noRegion>QLD 4072</wicri:noRegion></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 <italic>D<sub>2</sub></italic> statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, <italic>D<sub>2</sub></italic> 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. 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Rambaut</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcdonald, D" uniqKey="Mcdonald D">D. McDonald</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, C X" uniqKey="Chan C">C. X. Chan</name></author><author><name sortKey="Mahbob, M" uniqKey="Mahbob M">M. Mahbob</name></author><author><name sortKey="Ragan, M A" uniqKey="Ragan M">M. A. Ragan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stuart, G W" uniqKey="Stuart G">G. W. Stuart</name></author><author><name sortKey="Moffett, K" uniqKey="Moffett K">K. Moffett</name></author><author><name sortKey="Baker, S" uniqKey="Baker S">S. Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kupczok, A" uniqKey="Kupczok A">A. Kupczok</name></author><author><name sortKey="Schmidt, H" uniqKey="Schmidt H">H. Schmidt</name></author><author><name sortKey="Von Haeseler, A" uniqKey="Von Haeseler A">A. von Haeseler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bryant, D" uniqKey="Bryant D">D. Bryant</name></author><author><name sortKey="Steel, M" uniqKey="Steel M">M. Steel</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>France</li></country></list><tree><country name="Australie"><noRegion><name sortKey="Chan, Cheong Xin" sort="Chan, Cheong Xin" uniqKey="Chan C" first="Cheong Xin" last="Chan">Cheong Xin Chan</name></noRegion><name sortKey="Bernard, Guillaume" sort="Bernard, Guillaume" uniqKey="Bernard G" first="Guillaume" last="Bernard">Guillaume Bernard</name><name sortKey="Hogan, James M" sort="Hogan, James M" uniqKey="Hogan J" first="James M." last="Hogan">James M. Hogan</name><name sortKey="Poirion, Olivier" sort="Poirion, Olivier" uniqKey="Poirion O" first="Olivier" last="Poirion">Olivier Poirion</name><name sortKey="Ragan, Mark A" sort="Ragan, Mark A" uniqKey="Ragan M" first="Mark A." last="Ragan">Mark A. Ragan</name></country><country name="France"><noRegion><name sortKey="Poirion, Olivier" sort="Poirion, Olivier" uniqKey="Poirion O" first="Olivier" last="Poirion">Olivier Poirion</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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