Title:
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GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees
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Author:
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Kedzierska, A.M.; Casanellas Rius, Marta
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Other authors:
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Universitat Politècnica de Catalunya. Departament de Matemàtica Aplicada I; Universitat Politècnica de Catalunya. EGSA - Equacions Diferencials, Geometria, Sistemes Dinàmics i de Control, i Aplicacions |
Abstract:
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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. |
Subject(s):
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-Àrees temàtiques de la UPC::Matemàtiques i estadística -Markov processes -DNA -Markov, Processos de -ADN |
Rights:
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Attribution-NonCommercial-NoDerivs 3.0 Spain
http://creativecommons.org/licenses/by-nc-nd/3.0/es/ |
Document type:
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Article - Published version Article |
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