MAFFT on OpenStack - cdoorenweerd/PhylOStack GitHub Wiki
This HOWTO explains how to use MAFFT v7.237 on OpenStack with Ubuntu 14.04 LTS.
Note: This HOWTO assumes you have the PhylOStack installed and know how to start an instance, connect via SSH, transfer files and use screen sessions.
MAFFT requires an input alignment file in FASTA format, in the example named alignment.fas
Place the input file in a folder and copy this folder to the instance. Start a Screen session if desired, navigate to the folder with the input files and start a run by typing:
mafft --anysymbol --thread -1 alignment.fas > realigned_alignment.fasYou can use different parameters to change the behaviour of MAFFT, for which you should refer to the website: http://mafft.cbrc.jp/alignment/software/tips0.html