Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny?
Identifieur interne : 001147 ( Pmc/Curation ); précédent : 001146; suivant : 001148Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny?
Auteurs : Michael Höhl ; Mark A. RaganSource :
- Systematic Biology [ 1063-5157 ] ; 2007.
Abstract
The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from
Url:
DOI: 10.1080/10635150701294741
PubMed: 17454975
PubMed Central: 7107264
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny?</title><author><name sortKey="Hohl, Michael" sort="Hohl, Michael" uniqKey="Hohl M" first="Michael" last="Höhl">Michael Höhl</name><affiliation><nlm:aff id="au1"><institution>Australian Research Council Centre in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland</institution><addr-line>Brisbane, QLD 4072, Australia</addr-line> E-mail:<email>m.ragan@imb.uq.edu.au</email></nlm:aff></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><nlm:aff id="au1"><institution>Australian Research Council Centre in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland</institution><addr-line>Brisbane, QLD 4072, Australia</addr-line> E-mail:<email>m.ragan@imb.uq.edu.au</email></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17454975</idno><idno type="pmc">7107264</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107264</idno><idno type="RBID">PMC:7107264</idno><idno type="doi">10.1080/10635150701294741</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">001147</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001147</idno><idno type="wicri:Area/Pmc/Curation">001147</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001147</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny?</title><author><name sortKey="Hohl, Michael" sort="Hohl, Michael" uniqKey="Hohl M" first="Michael" last="Höhl">Michael Höhl</name><affiliation><nlm:aff id="au1"><institution>Australian Research Council Centre in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland</institution><addr-line>Brisbane, QLD 4072, Australia</addr-line> E-mail:<email>m.ragan@imb.uq.edu.au</email></nlm:aff></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><nlm:aff id="au1"><institution>Australian Research Council Centre in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland</institution><addr-line>Brisbane, QLD 4072, Australia</addr-line> E-mail:<email>m.ragan@imb.uq.edu.au</email></nlm:aff></affiliation></author></analytic><series><title level="j">Systematic Biology</title><idno type="ISSN">1063-5157</idno><idno type="eISSN">1076-836X</idno><imprint><date when="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from <ext-link ext-link-type="uri" xlink:href="http://www.bioinformatics.org.au">http://www.bioinformatics.org.au</ext-link> (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from <italic>k</italic>-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length <italic>k</italic> of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Beiko, R G" uniqKey="Beiko R">R. G. Beiko</name></author><author><name sortKey="Chan, C X" uniqKey="Chan C">C. X. Chan</name></author><author><name sortKey="Ragan, M A" uniqKey="Ragan M">M. A. Ragan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Beiko, R G" uniqKey="Beiko R">R. G. Beiko</name></author><author><name sortKey="Harlow, T J" uniqKey="Harlow T">T. J. Harlow</name></author><author><name sortKey="Ragan, M A" uniqKey="Ragan M">M. A. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Syst Biol</journal-id><journal-id journal-id-type="iso-abbrev">Syst. Biol</journal-id><journal-id journal-id-type="hwp">sysbio</journal-id><journal-id journal-id-type="publisher-id">sysbio</journal-id><journal-title-group><journal-title>Systematic Biology</journal-title></journal-title-group><issn pub-type="ppub">1063-5157</issn><issn pub-type="epub">1076-836X</issn><publisher><publisher-name>Society of Systematic Zoology</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">17454975</article-id><article-id pub-id-type="pmc">7107264</article-id><article-id pub-id-type="doi">10.1080/10635150701294741</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny?</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Höhl</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="au1">1</xref></contrib><contrib contrib-type="author"><name><surname>Ragan</surname><given-names>Mark A.</given-names></name><xref ref-type="aff" rid="au1">1</xref></contrib></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Page</surname><given-names>Rod</given-names></name><role>Associate Editor</role></contrib></contrib-group><aff id="au1"><label>1</label><institution>Australian Research Council Centre in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland</institution><addr-line>Brisbane, QLD 4072, Australia</addr-line> E-mail:<email>m.ragan@imb.uq.edu.au</email></aff><pub-date pub-type="ppub"><month>4</month><year>2007</year></pub-date><pub-date pub-type="epub" iso-8601-date="2007-04-01"><month>4</month><year>2007</year></pub-date><pub-date pub-type="pmc-release"><month>4</month><year>2007</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>56</volume><issue>2</issue><fpage>206</fpage><lpage>221</lpage><history><date date-type="received"><day>03</day><month>5</month><year>2006</year></date><date date-type="rev-recd"><day>18</day><month>7</month><year>2006</year></date><date date-type="accepted"><day>20</day><month>10</month><year>2006</year></date></history><permissions><copyright-statement>© 2007 Society of Systematic Biologists</copyright-statement><copyright-year>2007</copyright-year><license><license-p>This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.</license-p></license></permissions><self-uri xlink:href="56-2-206.pdf"></self-uri><abstract><title>Abstract</title><p>The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from <ext-link ext-link-type="uri" xlink:href="http://www.bioinformatics.org.au">http://www.bioinformatics.org.au</ext-link> (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from <italic>k</italic>-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length <italic>k</italic> of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.</p></abstract><kwd-group><kwd>Alignment-free methods</kwd><kwd>Bayesian</kwd><kwd>distance estimation</kwd><kwd>phylogenetics</kwd><kwd>tree reconstruction</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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