input, group1 and group2 must be in FASTA format.
mafft --maxiterate 1000 --seed group1 --seed group2 /dev/null [> output]
--auto
--6merpair
--globalpair
--localpair
--genafpair
--fastapair
--weighti number
--retree number
--maxiterate number
--fft
--nofft
--noscore
--memsave
--parttree
--dpparttree
--fastaparttree
--partsize number
--groupsize number
--op number
--ep number
--lop number
--lep number
--lexp number
--LOP number
--LEXP number
--bl number
--jtt number
--tm number
--aamatrix matrixfile
--fmodel
--clustalout
--inputorder
--reorder
--treeout
--quiet
--nuc
--amino
--seed alignment1 [--seed alignment2 --seed alignment3 ...]
Mafft stores the input sequences and other files in a temporary directory, which by default is located in /tmp.
MAFFT_BINARIES
FASTA_4_MAFFT
Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp>
Charles Plessy <charles-debian-nospam_at_plessy.org>
Mafft and its manpage are offered under the following conditions:
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.