Academic Journal
Efficient Based Estimation of Evolutionary Distance when Substitution Rates Vary Across Sites
| العنوان: | Efficient Based Estimation of Evolutionary Distance when Substitution Rates Vary Across Sites |
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| المؤلفون: | Guindon, Stéphane, Gascuel, Olivier |
| المساهمون: | Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) |
| المصدر: | ISSN: 0737-4038. |
| بيانات النشر: | HAL CCSD Oxford University Press (OUP) |
| سنة النشر: | 2002 |
| المجموعة: | Université de Montpellier: HAL |
| مصطلحات موضوعية: | Phylogeny, MESH: Algorithms, MESH: Amino Acid Substitution / genetics, MESH: Animals, MESH: Evolution, Molecular, MESH: Genetic Variation / genetics, MESH: Mutagenesis / genetics, MESH: Hemiptera / genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.GEN]Life Sciences [q-bio]/Genetics |
| الوصف: | International audience ; This paper deals with phylogenetic inference when the variability of substitution rates across sites (VRAS) is modeled by a gamma distribution. We show that underestimating VRAS, which results in underestimates for the evolutionary distances between sequences, usually improves the topological accuracy of phylogenetic tree inference by distance-based methods, especially when the molecular clock holds. We propose a method to estimate the gammashape parameter value which is most suited for tree topology inference, given the sequences at hand. This method is based on the pairwise evolutionary distances between sequences and allows one to reconstruct the phylogeny of a high number of taxa (>1,000). Simulation results show that the topological accuracy is highly improved when using the gamma shape parameter value given by our method, compared with the true (unknown) value which was used to generate the data. Furthermore, when VRAS is high, the topological accuracy of our distance-based method is better than that of a maximum likelihood approach. Finally, a data set of Maoricicada species sequences is analyzed, which confirms the advantage of our method. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/11919295; lirmm-00268454; https://hal-lirmm.ccsd.cnrs.fr/lirmm-00268454; https://hal-lirmm.ccsd.cnrs.fr/lirmm-00268454/document; https://hal-lirmm.ccsd.cnrs.fr/lirmm-00268454/file/mbev_19_04_534.pdf; PUBMED: 11919295 |
| DOI: | 10.1093/oxfordjournals.molbev.a004109 |
| الاتاحة: | https://hal-lirmm.ccsd.cnrs.fr/lirmm-00268454 https://hal-lirmm.ccsd.cnrs.fr/lirmm-00268454/document https://hal-lirmm.ccsd.cnrs.fr/lirmm-00268454/file/mbev_19_04_534.pdf https://doi.org/10.1093/oxfordjournals.molbev.a004109 |
| Rights: | http://creativecommons.org/licenses/by/ ; info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.DBDD8584 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/oxfordjournals.molbev.a004109 |
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