Cipres Science Gateway | MAFFT on TG Information

MAFFT on TG

The CIPRES Science Gateway offers a parallel version of MAFFT, a multiple alignment program run on Trestles. A complete description of parallel MAFFT is available here.This CIPRES Science Gateway submits to Trestles, alarge NSF Teragrid Resources. This machine allows your job to run for up to 168 hours (7 days).

How to use it: Submission to the TeraGrid requires the user to provide parameters that determine job priority in the queue, help identify the number of processors required, and set a time for job termination (whether the run is finished or not). First time users should view the primer on using TeraGrid resources here.

Disadvantages:The queue times on Teragrid resources vary according to traffic and according to the size of your job (shorter jobs typically have shorter queue waits). Sometimes TeraGrid resources go down for preventative maintenance or due to unforeseen circumstances. At present, this will cause your job to fail, and you will have to restart it. There is no restart capability at present.

Click this icon to check the traffic on TeraGrid:
Click this icon to check the Teragrid maintenance schedule:

A manual for MAFFT is available. [doc] [pdf]. MAFFT home page here.

If you use MAFFT, please cite (as appropriate):

Katoh, K.and Toh, H. (2010) "Parallelization of the MAFFT multiple sequence alignment program." Bioinformatics 26(15): 1899-1900.

Katoh, K., and Toh, H. (2007) "PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences." Bioinformatics 23:372-374. (describes the PartTree algorithm). [pdf]

Katoh, K., Kuma, K., Toh, H. and Miyata, T.(2005) "MAFFT version 5: improvement in accuracy of multiple sequence alignment." Nucl. Acids Res. 33:511-518. (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies) [pdf]

Katoh, K., Misawa, K., Kuma K., and Miyata, T.(2002) "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform." Nucleic Acids Res. 30:3059-3066. (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) [pdf]

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