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  MAFFT: a multiple sequence alignment program
  version 6.624beta, 2008/12/18

  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 (with make)
# cd core
# make install
# cd ..

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

By default, programs are installed into /usr/local/bin/ and 
some binaries are installed into /usr/local/lib/mafft/.


2. INSTALL (without make)
If you want to install the binaries to a different directory 
than /usr/local/lib/mafft/, 
% cp ./binaries/* /somewhere/else/

In this case, 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


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,