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  MAFFT: a multiple sequence alignment program
  version 6.240, 2007/04/04

  http://align.bmr.kyushu-u.ac.jp/mafft/software/
  katoh@bioreg.kyushu-u.ac.jp

  Copyright (c) 2006 Kazutaka Katoh
  Version 6.233 is distributed under the BSD license.
  See ./license/bsd.txt
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1. COMPILE
% cd src
% make clean
% make
% cd ..


2. INSTALL (using make)
# cd src
# make install
(Programs are installed into /usr/local/bin/ and 
 /usr/local/lib/mafft/.)


2. INSTALL (manual)
# mkdir -p /usr/local/lib/mafft/
# cp ./binaries/* /usr/local/lib/mafft/
# cp ./scripts/mafft /your/command/path/
# cp ./scripts/mafft-homologs.rb /your/command/path/
# cd /your/command/path/
# ln -s mafft fftns
# ln -s mafft fftnsi
# ln -s mafft nwns
# ln -s mafft nwnsi
# ln -s mafft linsi
# ln -s mafft ginsi
# ln -s mafft mafft-fftns
# ln -s mafft mafft-fftnsi
# ln -s mafft mafft-nwns
# ln -s mafft mafft-nwnsi
# ln -s mafft mafft-linsi
# ln -s mafft mafft-ginsi
# ln -s ../lib/mafft/mafft-profile .
(If you installed the binaries to a different directory than 
 /usr/local/lib/mafft, you have to set the MAFFT_BINARIES environment
 variable to the directory where the binaries are.)


3. CHECK
% cd test
% rehash
% setenv MAFFT_BINARIES /where/binaries/were/installed      # if necessary
% mafft sample > test.fftns2                                # FFT-NS-2
% mafft --maxiterate 100  sample > test.fftnsi              # FFT-NS-i
% mafft --globalpair sample > test.gins1                    # G-INS-1 
% mafft --globalpair --maxiterate 100  sample > test.ginsi  # G-INS-i 
% mafft --localpair sample > test.lins1                     # L-INS-1 
% mafft --localpair --maxiterate 100  sample > test.linsi   # L-INS-i 
% diff test.fftns2 sample.fftns2
% diff test.fftnsi sample.fftnsi
% diff test.gins1 sample.gins1
% diff test.ginsi sample.ginsi
% diff test.lins1 sample.lins1
% diff test.linsi sample.linsi


4. INPUT FORMAT
fasta format.

The type of input sequences (nucleotide or amino acid) is 
automatically recognized based on the frequency of A, T, G, C, U and N.

Size limit: 3,000,000 sites for linsi, ginsi and einsi.


5.  USAGE
% /usr/local/bin/mafft

-> http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/


6. UNINSTALL
# rm -r /usr/local/lib/mafft
# rm /usr/local/bin/mafft
# rm /usr/local/bin/fftns
# rm /usr/local/bin/fftnsi
# rm /usr/local/bin/nwns
# rm /usr/local/bin/nwnsi
# rm /usr/local/bin/linsi
# rm /usr/local/bin/ginsi
# rm /usr/local/bin/mafft-fftns
# rm /usr/local/bin/mafft-fftnsi
# rm /usr/local/bin/mafft-nwns
# rm /usr/local/bin/mafft-nwnsi
# rm /usr/local/bin/mafft-linsi
# rm /usr/local/bin/mafft-ginsi
# rm /usr/local/bin/mafft-profile
# rm /usr/local/bin/mafft-homologs.rb
