Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / mafft / readme

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+-----------------------------------------------------------------------
+  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,