Handel (bioinformatics software package)
From Wikipedia, the free encyclopedia
| Handel | |
|---|---|
| Developed by | Ian Holmes (UC Berkeley) |
| Latest release | 1 |
| OS | UNIX, Linux, Mac, Cygwin on Windows XP |
| Genre | Bioinformatics tool |
| Licence | Open source |
| Website | Handel homepage |
Handel is a suite of programs for multiple sequence alignment. Since it is based on a model of DNA sequence evolution that 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 DART software package. It accepts input files in Stockholm format.
[edit] References
- Holmes I, Bruno WJ. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics. 2001 Sep;17(9):803-20.
- Holmes I. Phylocomposer and Phylodirector: Analysis and Visualization of Transducer Indel Models. Bioinformatics. 2007
