source: branches/stable/GDE/MAFFT/mafft-7.055-with-extensions/readme

-----------------------------------------------------------------------
  MAFFT: a multiple sequence alignment program
  version 7.055beta, 2013/07/25

  http://mafft.cbrc.jp/alignment/software/
  kazutaka.katoh@aist.go.jp
-----------------------------------------------------------------------

1. COMPILE
     % cd core
     % make clean
     % make
     % cd ..

     To enable multithreading (linux only), 
     % cd core
     Uncomment line 8 of Makefile,
         ENABLE_MULTITHREAD = -Denablemultithread
     % make clean
     % make
     % cd ..
     
     If you have the './extensions' directory, which is for RNA alignments,
     % cd extensions
     % make clean
     % make
     % cd ..


2. INSTALL (select 2a or 2b [])
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/. Some binaries, which are not directly
     used by a user, are installed into /usr/local/libexec/mafft/.

     If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
     the binaries in the /somewhere/else/ directory are used, instead 
     of those in /usr/local/libexec/mafft/.

2b. Install without being root
     % cd core/
          Edit the first line of Makefile 
          From:
          PREFIX = ${PKGDIR}/usr/local
          To:
          PREFIX = /home/your_home/somewhere

          Edit the third line of Makefile 
          From:
          BINDIR = $(PREFIX)/bin
          To:
          BINDIR = /home/your_home/bin 
                   (or elsewhere in your command-search path)
     % make clean
     % make
     % make install

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

     The MAFFT_BINARIES environment variable *must not be* set.

     If the MAFFT_BINARIES environment variable is set to /somewhare/else/,
     it overrides the setting of PREFIX (/home/your_home/somewhere/ in the
     above example) in Makefile.

3. CHECK
     % cd test
     % rehash                                                   # 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.qinsi samplerna.qinsi
     % diff test.xinsi samplerna.xinsi

     If you use the multithread version, the results of iterative refinement
     methods (*-*-i) are not always identical.  Try this test with the single-
     thread mode (--thread 0).


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://mafft.cbrc.jp/alignment/software/


6. UNINSTALL
     # rm -r /usr/local/libexec/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-*
     # rm /usr/local/share/man/man1/mafft*


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

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