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This page was last updated on Thursday, 08-Dec-2016 09:45:16 CST

Installation notes for MAFFT version 7.305

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Prerequisites

Installation

  1. $ ver="7.305"
  2. $ cd /programinstallers/
  3. $ wget -N http://mafft.cbrc.jp/alignment/software/mafft-${ver}-with-extensions-src.tgz
  4. $ tar -zxvf mafft-${ver}-with-extensions-src.tgz
  5. $ cd mafft-${ver}-with-extensions/core
  6. "To enable multithreading, uncomment line 8 of Makefile" — it was already enabled, no changed needed
    ENABLE_MULTITHREAD = -Denablemultithread
  7. $ make clean ; make
  8. $ cd ../extensions
  9. $ make clean ; make
  10. $ cd ..
  11. Installation
    $ cd core
  12. $ sudo make install
  13. $ cd ../extensions
  14. $ sudo make install
  15. Cleanup
    $ cd /programinstallers
  16. $ rm mafft-${ver}-with-extensions -rf
    17. # 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/.

Contents of /usr/local/bin/ after installation 

-rwxr-xr-x  1 root  root      7781 Dec  8 09:36 mafft-sparsecore.rb
-rwxr-xr-x  1 root  root      8862 Dec  8 09:36 mafft-homologs.rb
-rwxr-xr-x  1 root  root     94069 Dec  8 09:36 mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 linsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 ginsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 fftns -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 nwnsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 nwns -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 fftnsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-linsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-ginsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-fftns -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 einsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-nwnsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-nwns -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-fftnsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-xinsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-qinsi -> mafft
lrwxrwxrwx  1 root  root         5 Dec  8 09:36 mafft-einsi -> mafft
lrwxrwxrwx  1 root  root        38 Dec  8 09:36 mafft-profile -> /usr/local/libexec/mafft/mafft-profile
lrwxrwxrwx  1 root  root        39 Dec  8 09:36 mafft-distance -> /usr/local/libexec/mafft/mafft-distance

Contents of /usr/local/libexec/mafft/ after installation 

-rwxr-xr-x 1 root root 678704 Dec  8 09:36 dvtditr
-rwxr-xr-x 1 root root 318224 Dec  8 09:36 dndfast7
-rwxr-xr-x 1 root root 318192 Dec  8 09:36 sextet5
-rwxr-xr-x 1 root root 318224 Dec  8 09:36 dndblast
-rwxr-xr-x 1 root root 318192 Dec  8 09:36 mafft-distance
-rwxr-xr-x 1 root root 645904 Dec  8 09:36 pairlocalalign
-rwxr-xr-x 1 root root 330512 Dec  8 09:36 multi2hat3s
-rwxr-xr-x 1 root root 621328 Dec  8 09:36 pairash
-rwxr-xr-x 1 root root 666384 Dec  8 09:36 addsingle
-rwxr-xr-x 1 root root 629520 Dec  8 09:36 splittbfast
-rwxr-xr-x 1 root root 666416 Dec  8 09:36 disttbfast
-rwxr-xr-x 1 root root 723760 Dec  8 09:36 tbfast
-rwxr-xr-x 1 root root 592656 Dec  8 09:36 mafft-profile
-rwxr-xr-x 1 root root 170640 Dec  8 09:36 f2cl
-rwxr-xr-x 1 root root 305936 Dec  8 09:36 mccaskillwrap
-rwxr-xr-x 1 root root  97008 Dec  8 09:36 countlen
-rwxr-xr-x 1 root root 301808 Dec  8 09:36 contrafoldwrap
-rwxr-xr-x 1 root root  97008 Dec  8 09:36 seq2regtable
-rwxr-xr-x 1 root root 232264 Dec  8 09:36 regtable2seq
-rwxr-xr-x 1 root root 297712 Dec  8 09:36 score
-rwxr-xr-x 1 root root 592656 Dec  8 09:36 getlag
-rwxr-xr-x 1 root root 301808 Dec  8 09:36 dndpre
-rwxr-xr-x 1 root root 592656 Dec  8 09:36 setcore
-rwxr-xr-x 1 root root 228184 Dec  8 09:36 replaceu
-rwxr-xr-x 1 root root 232264 Dec  8 09:36 restoreu
-rwxr-xr-x 1 root root 232272 Dec  8 09:36 setdirection
-rwxr-xr-x 1 root root   6312 Dec  8 09:36 version
-rwxr-xr-x 1 root root 641824 Dec  8 09:36 makedirectionlist
-rwxr-xr-x 1 root root  15541 Dec  8 09:36 seekquencer_premafft.pl
-rw-r--r-- 1 root root   4550 Dec  8 09:36 mafft-homologs.1
-rwxr-xr-x 1 root root  10475 Dec  8 09:36 mafftash_premafft.pl
-rw-r--r-- 1 root root  14771 Dec  8 09:36 mafft.1