+++ /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,
git://source.jalview.org / jabaws.git / blobdiff