Handel (bioinformatics software package)

Handel is a suite of programs for multiple sequence alignment.Since it is based on a model of DNA sequence evolutionthat explicitly incorporates insertion and deletion events,it effectively doubles as a program for ancestral sequence reconstruction.

The theory underpinning Handel is based on the finite state transducer, a concept borrowed from computational linguistics.

Handel can be downloaded as part of the [http://biowiki.org/DART DART software package] . It accepts input files in [http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html Stockholm] format.

References

* Holmes I, Bruno WJ. [http://www.ncbi.nlm.nih.gov/pubmed/11590097?dopt=Abstract Evolutionary HMMs: a Bayesian approach to multiple alignment] . Bioinformatics. 2001 Sep;17(9):803-20.
* Holmes I. [http://www.ncbi.nlm.nih.gov/pubmed/17804439?dopt=Abstract Phylocomposer and Phylodirector: Analysis and Visualization of Transducer Indel Models.] Bioinformatics. 2007

External links

* Handel [http://biowiki.org/HANDEL homepage] and [http://biowiki.org/StringTransducers theory]