Ir al contenido (pulsa Retorno)

Universitat Politècnica de Catalunya

    • Català
    • Castellano
    • English
    • LoginRegisterLog in (no UPC users)
  • mailContact Us
  • world English 
    • Català
    • Castellano
    • English
  • userLogin   
      LoginRegisterLog in (no UPC users)

UPCommons. Global access to UPC knowledge

Banner header
62.250 UPC E-Prints
You are here:
View Item 
  •   DSpace Home
  • E-prints
  • Grups de recerca
  • EGSA - Equacions Diferencials, Geometria, Sistemes Dinàmics i de Control, i Aplicacions
  • Articles de revista
  • View Item
  •   DSpace Home
  • E-prints
  • Grups de recerca
  • EGSA - Equacions Diferencials, Geometria, Sistemes Dinàmics i de Control, i Aplicacions
  • Articles de revista
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

Thumbnail
View/Open
1471-2105-13-216.pdf (160,0Kb)
 
10.1186/1471-2105-13-216
 
  View Usage Statistics
  LA Referencia / Recolecta stats
Cita com:
hdl:2117/17957

Show full item record
Kedzierska, A.M.
Casanellas Rius, MartaMés informacióMés informacióMés informació
Document typeArticle
Defense date2012-08-28
Rights accessOpen Access
Attribution-NonCommercial-NoDerivs 3.0 Spain
Except where otherwise noted, content on this work is licensed under a Creative Commons license : Attribution-NonCommercial-NoDerivs 3.0 Spain
Abstract
Background: 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.
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. 
URIhttp://hdl.handle.net/2117/17957
DOI10.1186/1471-2105-13-216
ISSN1471-2105
Publisher versionhttp://www.biomedcentral.com/1471-2105/13/216/abstract
Collections
  • EGSA - Equacions Diferencials, Geometria, Sistemes Dinàmics i de Control, i Aplicacions - Articles de revista [415]
  • Departament de Matemàtiques - Articles de revista [3.129]
  View Usage Statistics

Show full item record

FilesDescriptionSizeFormatView
1471-2105-13-216.pdf160,0KbPDFView/Open

Browse

This CollectionBy Issue DateAuthorsOther contributionsTitlesSubjectsThis repositoryCommunities & CollectionsBy Issue DateAuthorsOther contributionsTitlesSubjects

© UPC Obrir en finestra nova . Servei de Biblioteques, Publicacions i Arxius

info.biblioteques@upc.edu

  • About This Repository
  • Metadata under:Metadata under CC0
  • Contact Us
  • Send Feedback
  • Privacy Settings
  • Inici de la pàgina