MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

To incorporate protein structural information

% mafft --dash input > output
The input sequences are sent to the DASH sevice. Homologs with structural information are added and aligned with the original input sequences.

The added homologs can be excluded from the output by:

% mafft --dash --originalseqonly input > output

By default, the G-INS-i alignment strategy is used. Alignment strategy can be switched to L-INS-i by

% mafft --dash --localpair input > output

Can be combined with mafft-homologs.rb

% mafft-homologs.rb -l -d databasename -o '--dash' input > output
psiblast (in BLAST+) is required.

To enable this feature

All pre-compiled packages support this feature in versions ≥7.427. 

In the source package, the following procedure enables this feature.

  1. Edit  mafft-x.x/core/Makefile
    #DASH_CLIENT = dash_client
    DASH_CLIENT = dash_client
  2. Compile and install
    % cd mafft-x.x/core/
    % make clean
    % make
    % su
    # make install
    Go compiler is required.