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A 20-state empirical amino-acid substitution model for green plant chloroplasts

dc.contributor.authorCox, Cymon
dc.contributor.authorFoster, P. G.
dc.date.accessioned2014-10-27T14:32:27Z
dc.date.available2014-10-27T14:32:27Z
dc.date.issued2013
dc.date.updated2014-10-24T09:20:07Z
dc.description.abstractWe introduce a new empirical amino-acid substitution model intended for use with for green plant (Viridiplantae) chloroplast protein data, which we call gcpREV (green chloroplast reversible model). Relative exchange rates and base composition frequencies among amino-acids were calculated using a Markov-chain Monte Carlo analysis on a combined data set of 34 proteins sampled among 27 taxa of green plants. The gcpREV model is a better fit than the commonly-used cpREV model to five previously published chloroplast protein test data sets of green plants, but is not a better fit to test data consisting mostly of non-green plant chloroplasts. Consequently, our analyses suggest a degree of specificity of the new model to green plant chloroplast data. The new model is implemented in the software P4, and model description files are available for other popular phylogenetic analysis software.por
dc.identifier.citationCox, C.J.; Foster, P.G.A 20-state empirical amino-acid substitution model for green plant chloroplasts, Molecular Phylogenetics and Evolution, 68, 2, 218-220, 2013.por
dc.identifier.doihttp://dx.doi.org/ 10.1016/j.ympev.2013.03.030
dc.identifier.issn1055-7903
dc.identifier.urihttp://hdl.handle.net/10400.1/5527
dc.language.isoengpor
dc.peerreviewedyespor
dc.publisherElsevierpor
dc.relation.publisherversionhttp://www.sciencedirect.com/science/article/pii/S1055790313001395por
dc.subjectPhylogeny reconstructionpor
dc.subjectGreen plantpor
dc.subjectChloroplastpor
dc.subjectEmpirical protein modelpor
dc.subjectgcpREVpor
dc.subjectcpREVpor
dc.titleA 20-state empirical amino-acid substitution model for green plant chloroplastspor
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage220por
oaire.citation.issue2por
oaire.citation.startPage218por
oaire.citation.titleMolecular Phylogenetics and Evolutionpor
oaire.citation.volume68por
person.familyNameCox
person.givenNameCymon
person.identifier.ciencia-id6B15-9771-1D04
person.identifier.orcid0000-0002-4927-979X
person.identifier.ridD-1303-2012
person.identifier.scopus-author-id7402112716
rcaap.rightsrestrictedAccesspor
rcaap.typearticlepor
relation.isAuthorOfPublication82c3689c-60b6-440d-9d7b-49e6dbd6861b
relation.isAuthorOfPublication.latestForDiscovery82c3689c-60b6-440d-9d7b-49e6dbd6861b

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