ROSE, a program simulating evolution of sequences using a
probabilistic model, was used alongside BALIBASE. A tree guides
the evolution of sequences from a common ancestor using insertions,
deletions and substitutions. As all events in the history of
the sequences are known, the true multiple sequence alignment
is created on the fly. In the artificial evolution, we can specify many
parameters, such as sequence length, evolutionary distance and
evolutionary ancestors, to generate sequences of biological signifi-
cance. Sequences generated by ROSE are suitable for multiple
alignments and widely used in prediction of relationship between
biological evolutions.