MAFFT: a multiple sequence alignment program version 7.471, 2020/Jul/3

http://mafft.cbrc.jp/alignment/software/ katoh@ifrec.osaka-u.ac.jp

1. COMPILE To use Visual C++ compiler (Windows only): % set CC=cl

   % 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 to /usr/local/ using root account

   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 to non-default location (root account is not necessary) % cd core/ Edit the first line of Makefile From: PREFIX = /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 = /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,