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MAFFT

MAFFT

Description

MAFFT is a fast and accurate multiple sequence alignment program for protein and nucleotide sequences. MAFFT offers several different alignment strategies from which user should select the most suitable for his case.


Available

Version on CSC's Servers

Taito: 7.407
Chipster graphical user interface


Usage

To set up the MAFFT commands in Taito give command :

module load biokit/4.9.3

After this you can use MAFFT with command syntax:

mafft --parametes input_file.fasta > aligned_output.fasta

The most commonly used alignment strategies have their own command aliases. Part of them are listed below:

L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information)

mafft --localpair --maxiterate 1000 input > output

linsi input > output (Alias; works the same as the above) 

G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):

mafft --globalpair --maxiterate 1000 input > output

ginsi input > output (Alias)

E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):

mafft --ep 0 --genafpair --maxiterate 1000 input > output

einsi input > output (Alias)

Alignment of two alignments

mafft-profile group1 group2 > output

 


Discipline

Biosciences

References


Support

servicedesk@csc.fi


Manual