Bioinformatics, Vol 14, 157-163, Copyright © 1998 by Oxford University Press
J Stoye, D Evers and F Meyer
MOTIVATION: We present a new probabilistic model of the evolution of RNA-,
DNA-, or protein-like sequences and a software tool, Rose, that implements
this model. Guided by an evolutionary tree, a family of related sequences
is created from a common ancestor sequence by insertion, deletion and
substitution of characters. During this artificial evolutionary process,
the 'true' history is logged and the 'correct' multiple sequence alignment
is created simultaneously. The model also allows for varying rates of
mutation within the sequences, making it possible to establish so-called
sequence motifs. RESULTS: The data created by Rose are suitable for the
evaluation of methods in multiple sequence alignment computation and the
prediction of phylogenetic relationships. It can also be useful when
teaching courses in or developing models of sequence evolution and in the
study of evolutionary processes. AVAILABILITY: Rose is available on the
Bielefeld Bioinformatics WebServer under the following URL:
http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/ The source code is available
upon request. Contact: folker@TechFak.Uni-Bielefeld.DE
ARTICLES
Rose: generating sequence families
Research Center for Interdisciplinary Studies on Structure Formation (FSPM), University of Bielefeld, Postfach, Germany.
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