Show simple item record

dc.contributor.authorKedzierska, A.M.
dc.contributor.authorCasanellas Rius, Marta
dc.contributor.otherUniversitat Politècnica de Catalunya. Departament de Matemàtica Aplicada I
dc.date.accessioned2013-02-25T12:43:58Z
dc.date.available2013-02-25T12:43:58Z
dc.date.created2012-08-28
dc.date.issued2012-08-28
dc.identifier.citationKedzierska, A.; Casanellas, M. GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees. "BMC bioinformatics", 28 Agost 2012, vol. 13, núm. 216, p. 1-4.
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/2117/17957
dc.description.abstractBackground: A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). Results: We present the first package designed to generate MSAs evolving under discrete-time Markov processes on phylogenetic trees, directly from probability substitution matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site), the algorithm produces DNA alignments of desired length. GenNon-h is publicly available for download. Conclusion: The software presented here is an efficient tool to generate DNA MSAs on a given phylogenetic tree. GenNon-h provides the user with the nonstationary or nonhomogeneous phylogenetic data that is well suited for testing complex biological hypotheses, exploring the limits of the reconstruction algorithms and their robustness to such models.
dc.format.extent4 p.
dc.language.isoeng
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.subjectÀrees temàtiques de la UPC::Matemàtiques i estadística
dc.subject.lcshMarkov processes
dc.subject.lcshDNA
dc.titleGenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees
dc.typeArticle
dc.subject.lemacMarkov, Processos de
dc.subject.lemacADN
dc.contributor.groupUniversitat Politècnica de Catalunya. EGSA - Equacions Diferencials, Geometria, Sistemes Dinàmics i de Control, i Aplicacions
dc.identifier.doi10.1186/1471-2105-13-216
dc.relation.publisherversionhttp://www.biomedcentral.com/1471-2105/13/216/abstract
dc.rights.accessOpen Access
local.identifier.drac11068360
dc.description.versionPostprint (published version)
local.citation.authorKedzierska, A.; Casanellas, M.
local.citation.publicationNameBMC bioinformatics
local.citation.volume13
local.citation.number216
local.citation.startingPage1
local.citation.endingPage4
dc.identifier.pmid22928840


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record