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
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001147
Links to Exploration step
PMC:7107264Le document en format XML
<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. Ragan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Beiko, R G" uniqKey="Beiko R">R. G. Beiko</name>
</author>
<author><name sortKey="Keith, J M" uniqKey="Keith J">J. M. Keith</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. Ragan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Blaisdell, B E" uniqKey="Blaisdell B">B. E. Blaisdell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Castresana, J" uniqKey="Castresana J">J. Castresana</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chu, K H" uniqKey="Chu K">K. H. Chu</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J. Qi</name>
</author>
<author><name sortKey="Yu, Z G" uniqKey="Yu Z">Z.-G. Yu</name>
</author>
<author><name sortKey="Anh, V" uniqKey="Anh V">V. Anh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cowles, M K" uniqKey="Cowles M">M. K. Cowles</name>
</author>
<author><name sortKey="Carlin, B P" uniqKey="Carlin B">B. P. Carlin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edgar, R C" uniqKey="Edgar R">R. C. Edgar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edgar, R C" uniqKey="Edgar R">R. C. Edgar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Felsenstein, J" uniqKey="Felsenstein J">J. Felsenstein</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Felsenstein, J" uniqKey="Felsenstein J">J. Felsenstein</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gelman, A" uniqKey="Gelman A">A. Gelman</name>
</author>
<author><name sortKey="Carlin, J B" uniqKey="Carlin J">J. B. Carlin</name>
</author>
<author><name sortKey="Stern, H S" uniqKey="Stern H">H. S. Stern</name>
</author>
<author><name sortKey="Rubin, D B" uniqKey="Rubin D">D. B. Rubin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hall, B G" uniqKey="Hall B">B. G. Hall</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hao, B" uniqKey="Hao B">B. Hao</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J. Qi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Harlow, T J" uniqKey="Harlow T">T. J. Harlow</name>
</author>
<author><name sortKey="Gogarten, J P" uniqKey="Gogarten J">J. P. Gogarten</name>
</author>
<author><name sortKey="Ragan, M A" uniqKey="Ragan M">M. A. Ragan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Henikoff, S" uniqKey="Henikoff S">S. Henikoff</name>
</author>
<author><name sortKey="Henikoff, J G" uniqKey="Henikoff J">J. G. Henikoff</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hohl, M" uniqKey="Hohl M">M. Höhl</name>
</author>
<author><name sortKey="Rigoutsos, I" uniqKey="Rigoutsos I">I. Rigoutsos</name>
</author>
<author><name sortKey="Ragan, M A" uniqKey="Ragan M">M. A. Ragan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huelsenbeck, J P" uniqKey="Huelsenbeck J">J. P. Huelsenbeck</name>
</author>
<author><name sortKey="Ronquist, F" uniqKey="Ronquist F">F. Ronquist</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jones, D T" uniqKey="Jones D">D. T. Jones</name>
</author>
<author><name sortKey="Taylor, W R" uniqKey="Taylor W">W. R. Taylor</name>
</author>
<author><name sortKey="Thornton, J M" uniqKey="Thornton J">J. M. Thornton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lempel, A" uniqKey="Lempel A">A. Lempel</name>
</author>
<author><name sortKey="Ziv, J" uniqKey="Ziv J">J. Ziv</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lewis, P O" uniqKey="Lewis P">P. O. Lewis</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, M" uniqKey="Li M">M. Li</name>
</author>
<author><name sortKey="Badger, J H" uniqKey="Badger J">J. H. Badger</name>
</author>
<author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name>
</author>
<author><name sortKey="Kwong, S" uniqKey="Kwong S">S. Kwong</name>
</author>
<author><name sortKey="Kearney, P" uniqKey="Kearney P">P. Kearney</name>
</author>
<author><name sortKey="Zhang, H" uniqKey="Zhang H">H. Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mantaci, S" uniqKey="Mantaci S">S. Mantaci</name>
</author>
<author><name sortKey="Restivo, A" uniqKey="Restivo A">A. Restivo</name>
</author>
<author><name sortKey="Rosone, G" uniqKey="Rosone G">G. Rosone</name>
</author>
<author><name sortKey="Sciortino, M" uniqKey="Sciortino M">M. Sciortino</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nee, S" uniqKey="Nee S">S. Nee</name>
</author>
<author><name sortKey="May, R M" uniqKey="May R">R. M. May</name>
</author>
<author><name sortKey="Harvey, P H" uniqKey="Harvey P">P. H. Harvey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ogden, T H" uniqKey="Ogden T">T. H. Ogden</name>
</author>
<author><name sortKey="Rosenberg, M S" uniqKey="Rosenberg M">M. S. Rosenberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Otu, H H" uniqKey="Otu H">H. H. Otu</name>
</author>
<author><name sortKey="Sayood, K" uniqKey="Sayood K">K. Sayood</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Qi, J" uniqKey="Qi J">J. Qi</name>
</author>
<author><name sortKey="Wang, B" uniqKey="Wang B">B. Wang</name>
</author>
<author><name sortKey="Hao, B I" uniqKey="Hao B">B.-I. Hao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A. Rambaut</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A. Rambaut</name>
</author>
<author><name sortKey="Grassly, N C" uniqKey="Grassly N">N. C. Grassly</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rigoutsos, I" uniqKey="Rigoutsos I">I. Rigoutsos</name>
</author>
<author><name sortKey="Floratos, A" uniqKey="Floratos A">A. Floratos</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robinson, D F" uniqKey="Robinson D">D. F. Robinson</name>
</author>
<author><name sortKey="Foulds, L R" uniqKey="Foulds L">L. R. Foulds</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ronquist, F" uniqKey="Ronquist F">F. Ronquist</name>
</author>
<author><name sortKey="Huelsenback, J P" uniqKey="Huelsenback J">J. P. Huelsenback</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Saitou, N" uniqKey="Saitou N">N. Saitou</name>
</author>
<author><name sortKey="Nei, M" uniqKey="Nei M">M. Nei</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stuart, G W" uniqKey="Stuart G">G. W. Stuart</name>
</author>
<author><name sortKey="Berry, M W" uniqKey="Berry M">M. W. Berry</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stuart, G W" uniqKey="Stuart G">G. W. Stuart</name>
</author>
<author><name sortKey="Berry, M W" uniqKey="Berry M">M. W. Berry</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="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="Leader, J J" uniqKey="Leader J">J. J. Leader</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Taylor, W R" uniqKey="Taylor W">W. R. Taylor</name>
</author>
<author><name sortKey="Jones, D T" uniqKey="Jones D">D. T. Jones</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ulitsky, I" uniqKey="Ulitsky I">I. Ulitsky</name>
</author>
<author><name sortKey="Burstein, D" uniqKey="Burstein D">D. Burstein</name>
</author>
<author><name sortKey="Tuller, T" uniqKey="Tuller T">T. Tuller</name>
</author>
<author><name sortKey="Chor, B" uniqKey="Chor B">B. Chor</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Van Helden, J" uniqKey="Van Helden J">J. Van Helden</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vinga, S" uniqKey="Vinga S">S. Vinga</name>
</author>
<author><name sortKey="Almeida, J" uniqKey="Almeida J">J. Almeida</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vinga, S" uniqKey="Vinga S">S. Vinga</name>
</author>
<author><name sortKey="Gouveia Oliveira, R" uniqKey="Gouveia Oliveira R">R. Gouveia-Oliveira</name>
</author>
<author><name sortKey="Almeida, J S" uniqKey="Almeida J">J. S. Almeida</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wang, L" uniqKey="Wang L">L. Wang</name>
</author>
<author><name sortKey="Jiang, T" uniqKey="Jiang T">T. Jiang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wu, T J" uniqKey="Wu T">T.-J. Wu</name>
</author>
<author><name sortKey="Burke, J P" uniqKey="Burke J">J. P. Burke</name>
</author>
<author><name sortKey="Davison, D B" uniqKey="Davison D">D. B. Davison</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yang, A C C" uniqKey="Yang A">A. C.-C. Yang</name>
</author>
<author><name sortKey="Goldberger, A L" uniqKey="Goldberger A">A. L. Goldberger</name>
</author>
<author><name sortKey="Peng, C K" uniqKey="Peng C">C.-K. Peng</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yu, Z G" uniqKey="Yu Z">Z.-G. Yu</name>
</author>
<author><name sortKey="Anh, V" uniqKey="Anh V">V. Anh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zar, J H" uniqKey="Zar J">J. H. Zar</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<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 . </pmc-comment>
<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)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001147 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 001147 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Pmc |étape= Curation |type= RBID |clé= PMC:7107264 |texte= Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny? }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:17454975" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |