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Open Access Software

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

Anna M Kedzierska12 and Marta Casanellas2*

Author Affiliations

1 Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain

2 Departament de Matemàtica Aplicada I, ETSEIB, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, 08028 Barcelona, Spain

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BMC Bioinformatics 2012, 13:216  doi:10.1186/1471-2105-13-216

Published: 28 August 2012



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).


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.


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.