title: Rose: generating sequence families.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  folker@TechFak.Uni-Bielefeld.DE
authors.affiliation: Research Center for Interdisciplinary Studies on Structure Formation (FSPM), University of Bielefeld, Postfach, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Stoye
authors.forename: D
authors.initials: D
authors.lastname: Evers
authors.forename: F
authors.initials: F
authors.lastname: Meyer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D012313:RNA / Q000235:genetics; D016415:Sequence Alignment; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA