Removing old version of mafft to replace with the new

[jabaws.git] / binaries / src / mafft / readme

diff --git a/binaries/src/mafft/readme b/binaries/src/mafft/readme
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------------------------------------------------------------------------
-  MAFFT: a multiple sequence alignment program
-  version 6.713beta, 2009/09/24
-
-  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 (select one procedure from 2a, 2b and 2c)
-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/ and some binaries are installed into 
-     /usr/local/lib/mafft/.
-
-     If you want to install the binaries to a different directory 
-     than /usr/local/lib/mafft/, select either of the following
-     two procedure (2b and 2c).
-
-2b. Install without being root
-     % cp ./binaries/* /somewhere/else/
-
-     In this case (2b), 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
-
-2c. Install without being root
-     % cd core/
-          Edit the first line of Makefile 
-          From:
-          PREFIX = /usr/local
-          To:
-          PREFIX = /home/your_home/somewhere
-     % 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
-
-     In this case (2c), the MAFFT_BINARIES environment variable 
-     *must not be* set.
-
-
-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,