Background#R##N#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).
['Anna M Kedzierska', 'Marta Casanellas']
GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees