Sep 252013
 

SATCHMO 2.06 / SATCHMO-JS

:: DESCRIPTION

SATCHMO uses HMM-HMM scoring and alignment to simultaneously estimate a phylogenetic tree and a multiple sequence alignment (MSA).

SATCHMO-JS is a variant of the SATCHMO algorithm designed for scalability to large datasets. We use a jump-start (JS) protocol to reduce complexity, employing computationally efficient MSA methods for subgroups of closely related sequences and saving the computationally expensive HMM-HMM scoring and alignment to estimate the tree and MSA between more distantly related subgroups.

::DEVELOPER

the Berkeley Phylogenomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Python
  • BioPython

:: DOWNLOAD

  SATCHMO / SATCHMO-JS

:: MORE INFORMATION

Citation

Edgar, R., and Sjölander, K.,
SATCHMO: Sequence Alignment and Tree Construction using Hidden Markov models
Bioinformatics. 2003 Jul 22; 19(11):1404-11.

Hagopian, R., Davidson, J., Datta, R., Samad, B., Jarvis, G., and Sjölander, K.
“SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction”,
Nucl. Acids Res. (2010) 38(suppl 2): W29-W34., doi:10.1093/nar/gkq298

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