| ----------------------------------------------------------------------- |
| MAFFT: a multiple sequence alignment program |
| version 6.624beta, 2008/12/18 |
| |
| http://align.bmr.kyushu-u.ac.jp/mafft/software/ |
| katoh@bioreg.kyushu-u.ac.jp |
| ----------------------------------------------------------------------- |
| |
| 1. COMPILE |
| % cd core |
| % make clean |
| % make |
| % cd .. |
| |
| If you have the './extensions' directory, which is for RNA alignments, |
| % cd extensions |
| % make clean |
| % make |
| % cd .. |
| |
| |
| 2. INSTALL (with make) |
| # cd core |
| # make install |
| # cd .. |
| |
| If you have the './extensions' directory, |
| # cd extensions |
| # make install |
| # cd .. |
| |
| By default, programs are installed into /usr/local/bin/ and |
| some binaries are installed into /usr/local/lib/mafft/. |
| |
| |
| 2. INSTALL (without make) |
| If you want to install the binaries to a different directory |
| than /usr/local/lib/mafft/, |
| % cp ./binaries/* /somewhere/else/ |
| |
| In this case, you have to set the MAFFT_BINARIES environment |
| variable to point to the directory where the binaries are. |
| % setenv MAFFT_BINARIES /somewhere/else/ # for csh, tcsh |
| $ export MAFFT_BINARIES=/somewhere/else/ # for sh, bash |
| |
| |
| 3. CHECK |
| % cd test |
| % rehash # if necessary |
| % setenv MAFFT_BINARIES /where/binaries/were/installed # 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.linsi sample.linsi |
| % diff test.qinsi sample.qinsi |
| % diff test.xinsi sample.xinsi |
| |
| |
| 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://align.bmr.kyushu-u.ac.jp/mafft/software/ |
| |
| |
| 6. UNINSTALL |
| # rm -r /usr/local/lib/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-* |
| |
| |
| 7. LICENSE |
| See the './license' file. |
| |
| If you have the extensions, see the './license.extensions' file, |
