title: Phylocomposer and phylodirector: analysis and visualization of transducer indel models.
abstract: Finite-state string transducers are probabilistic tools similar to Hidden Markov Models that can be systematically extended to large number of sequences related by indel and substitution processes on phylogenetic trees. The number of states in such models grows exponentially with the number of nodes in the tree, with the consequence that even quite small trees can be difficult to analyze or visualize. Here, we present two tools, phylocomposer and phylodirector, for working with string transducers. The former tool implements previously described composition algorithms for extending transducers to arbitrary tree topologies, while the latter generates short animations for arbitrary input alignments and phylogenetic trees, illustrating the state path through the composed transducer.
  
  
  BACKGROUND
  Phylocomposer and phylodirector are freely available at http://biowiki.org/PhyloComposer and http://biowiki.org/PhyloDirector
authors.affiliation: Department of Bioengineering, University of California, Berkeley, CA, USA. ihh@berkeley.edu
authors.forename: Ian
authors.initials: I
authors.lastname: Holmes
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D019143:Evolution, Molecular; D054643:INDEL Mutation / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D014159:Transducers; D014584:User-Computer Interface