--- /dev/null
+-----------------------------------------------------------------------
+ MAFFT: a multiple sequence alignment program
+ version 6.857beta, 2011/05/30
+
+ 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,