Linked Life Data

11919295

Source:http://linkedlifedata.com/resource/pubmed/id/11919295

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2002-3-28
pubmed:abstractText
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 gamma shape 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.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
0737-4038
pubmed:author
pubmed:issnType
Print
pubmed:volume
19
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
534-43
pubmed:dateRevised
2008-11-21
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Efficient biased estimation of evolutionary distances when substitution rates vary across sites.
pubmed:affiliation
LIRMM, UMR 9928 Université Montpellier II/CNRS, 161 Rue Ada, 34392 Montpellier Cedex 5, France.
pubmed:publicationType
Journal Article, Comparative Study