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Rose - random model of sequence evolution - Version 1.3


Rose implements a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences.
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.
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.

If you use Rose in your own research, please cite:
Rose: generating sequence families
J. Stoye, D. Evers, F. Meyer
in: Bioinformatics - (formerly CABIOS), Volume 14, Issue 2, March 1998, pp. 157-163, OUP Press
HTML abstract (10 KB) or Full-text PDF (168 KB)


GEvolutionS


GEvolutions simulates an evolutionary genome rearrangement szenario with different genome rearrangement operations. It operates on the most general model of genomes with a mixed collection on linear and circular chromosomes. The simulation process includes all classical rearrangement operations such dcj, fission, fusion, inversion, translocation and transposition with a choosable quantum to appear with.
Click here to use GEvolutionS

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Fri Dec 14 13:01:22 2012