Phylogenies from whole genomes: Methodological update within a distance-based framework

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Show simple item record Auch, Alexander F. de_DE Henz, Stefan R. de_DE Göker, Markus de_DE 2008-06-26 de_DE 2014-03-18T10:18:47Z 2008-06-26 de_DE 2014-03-18T10:18:47Z 2006 de_DE
dc.identifier.other 394146220 de_DE
dc.identifier.uri de_DE
dc.description.abstract Methods which derive pairwise distances directly from complete sequenced genomes are a potentially important and efficient tool within the growing field of phylogenomics.We have shown in two previous studies that the Genome BLAST Distance Phylogeny (GBDP) approach leads to reliable phylogenetic estimates if applied to prokaryotic as well as plastid and mitochondrial genomes. Basically, GBDP first invokes tools such as BLAST to identify high-scoring segment pairs (HSPs) between all pairs of genomes; afterwards, pairwise distances are estimated based on different formulae. Here, we examine (1) a new GBDP distance formula, based on a combination of two previously existing ones; (2) use of BLAT instead of BLASTN and TBLASTX HSP search; (3) an alternative measure for the agreement of a distance matrix with a predefined reference topology; (4) alternative topology-independent measures of distance quality per se. All examinations were based on a enlarged dataset compared to that used in our previous study, additionally containing interesting key taxa. en
dc.language.iso en de_DE
dc.publisher Universität Tübingen de_DE
dc.rights ubt-podok de_DE
dc.rights.uri de_DE
dc.rights.uri en
dc.subject.classification Phylogenie de_DE
dc.subject.ddc 570 de_DE
dc.subject.other Phylogeny , Whole genome Phylogeny , Phylogenetic Methods en
dc.title Phylogenies from whole genomes: Methodological update within a distance-based framework en
dc.type WorkingPaper de_DE 2008-06-26 de_DE
utue.publikation.fachbereich Informatik de_DE
utue.publikation.fachbereich Sonstige/Externe de_DE
utue.publikation.fachbereich Biologie de_DE
utue.publikation.fakultaet 7 Mathematisch-Naturwissenschaftliche Fakultät de_DE
utue.publikation.fakultaet 9 Sonstige / Externe de_DE
dcterms.DCMIType Text de_DE
utue.publikation.typ workingPaper de_DE 3417 de_DE


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