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  MAFFT: a multiple sequence alignment program
  version 6.713beta, 2009/09/24

  http://align.bmr.kyushu-u.ac.jp/mafft/software/
  katoh@bioreg.kyushu-u.ac.jp
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1. COMPILE
     % cd core
     % make clean
     % make
     % cd ..

     If you have the './extensions' directory, which is for RNA alignments,
     % cd extensions
     % make clean
     % make
     % cd ..


2. INSTALL (select one procedure from 2a, 2b and 2c)
2a. Install as root
     # cd core
     # make install
     # cd ..

     If you have the './extensions' directory,
     # cd extensions 
     # make install
     # cd ..

     By this procedure (2a), programs are installed into 
     /usr/local/bin/ and some binaries are installed into 
     /usr/local/lib/mafft/.

     If you want to install the binaries to a different directory 
     than /usr/local/lib/mafft/, select either of the following
     two procedure (2b and 2c).

2b. Install without being root
     % cp ./binaries/* /somewhere/else/

     In this case (2b), you *have to set* the MAFFT_BINARIES environment 
     variable to point to the directory where the binaries are.
     % setenv MAFFT_BINARIES /somewhere/else/  # for csh, tcsh
     $ export MAFFT_BINARIES=/somewhere/else/  # for sh, bash

2c. Install without being root
     % cd core/
          Edit the first line of Makefile 
          From:
          PREFIX = /usr/local
          To:
          PREFIX = /home/your_home/somewhere
     % make clean
     % make
     % make install

     If you have the './extensions' directory,
     % cd extensions/
          Edit the first line of Makefile 
          From:
          PREFIX = /usr/local
          To:
          PREFIX = /home/your_home/somewhere
     % make clean
     % make
     % make install

     In this case (2c), the MAFFT_BINARIES environment variable 
     *must not be* set.


3. CHECK
     % cd test
     % rehash                                                   # if necessary
     % 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

     If you have the './extensions' directory,
     % mafft-qinsi samplerna > test.qinsi                       # Q-INS-i
     % mafft-xinsi samplerna > test.xinsi                       # X-INS-i
     % diff test.linsi sample.linsi
     % diff test.qinsi sample.qinsi
     % diff test.xinsi sample.xinsi


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.


5.  USAGE
     % /usr/local/bin/mafft input > output

See also http://align.bmr.kyushu-u.ac.jp/mafft/software/


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-*


7. LICENSE
     See the './license' file.

     If you have the extensions, see the './license.extensions' file,