Software:Handel (bioinformatics software package)
From HandWiki
| Developer(s) | Ian Holmes (UC Berkeley) |
|---|---|
| Stable release | 1
|
| Operating system | UNIX, Linux, Mac, Cygwin on Windows XP |
| Type | 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.
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
External links
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