A number of software packages are available to
generate DNA 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).
GenNon-H is the first package designed to generate multiple sequence alignments under
the discrete-time Markov processes on phylogenetic trees, which samples directly from the transition 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 a collaborative project described at http://genome.crg.es/cgi-bin/phylo_mod_sel/AlgGenNonH.pl.
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