
                                    ROSE

                     Random-model Of Sequence Evolution 

                 Rose implements a new probabilistic model of
                  RNA-, DNA-, or protein-sequence evolution.

             URL http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/


Rose Copyright (c) 1997-2000 University of Bielefeld, Germany and
Deutsches Krebsforschungszentrum (DKFZ) Heidelberg, Germany.
Please see the file COPYING for details.
For documentation, please see the files in the doc subdirectory.
For building and installation instructions please see the INSTALL file.


ABSTRACT
========

Rose: generating sequence families

Jens Stoye (1) Dirk Evers (2) and Folker Meyer (2) 

1 Research Center for Interdisciplinary Studies on Structure Formation (FSPM)
2 Technische Fakultaet
  University of Bielefeld, Postfach 100 131, 33501 Bielefeld, Germany 

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.

For a complete description of the functionality of ROSE see:

Stoye, J., Evers, D., & Meyer, F. (1998)
Rose: generating sequence families.
In Bioinformatics, Vol. 14, Issue 2, pp. 157-163.

http://www.oup.co.uk/bioinformatics/hdb/Volume_14/Issue_02/ps/btb005_gml.ps.gz

preprint version:
ftp://ftp.uni-bielefeld.de/pub/papers/techfak/pi/Report97-04.ps.gz


OBTAINING ROSE
==============

The latest version of rose is available on our ftp at
ftp://ftp.Uni-Bielefeld.DE/pub/projects/techfak/pi/rose/

