Cipres Science Gateway | MAFFT on TG Information

MAFFT on XSEDE

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. The CIPRES Science Gateway submits to Trestles, a large NSF XSEDE Resource. This machine allows your job to run for up to 168 hours (7 days).

How to use it: Submission to XSEDE 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 XSEDE resources here.

Disadvantages:The queue times on XSEDE resources vary according to traffic and according to the size of your job (shorter jobs typically have shorter queue waits). Sometimes XSEDE 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 XSEDE:
Click this icon to check the XSEDE 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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