2026-04-14T03:08:35Zhttps://recercat.cat/oai/requestoai:recercat.cat:2117/179572026-01-26T02:07:34Zcom_2072_1033col_2072_452950
RECERCAT
author
Kedzierska, A.M.
author
Casanellas Rius, Marta
2012-08-28
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.Postprint (published version)
http://creativecommons.org/licenses/by-nc-nd/3.0/es/ Open Access Attribution-NonCommercial-NoDerivs 3.0 Spain
Àrees temàtiques de la UPC::Matemàtiques i estadística
Markov processes
DNA
Markov, Processos de
ADN
GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees
Article