----------------------------------------------------------------------- MAFFT: a multiple sequence alignment program version 7.305beta, 2016/Aug/16 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 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,