RapidNJ 2.3.2 – Fast Canonical Neighbor-joining Tree Construction

RapidNJ 2.3.2

:: DESCRIPTION

RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.

::DEVELOPER

RapidNJ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 RapidNJ

:: MORE INFORMATION

Citation:

Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen.
Rapid Neighbour Joining.
In Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, Springer Verlag, October 2008. doi:10.1007/978-3-540-87361-7_10

SATCHMO 2.06 / SATCHMO-JS – Simultaneous Alignment and Tree Construction using Hidden Markov Models

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