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How to add /usr/local/bin/ to command-search path

MAFFT is installed into the /usr/local/bin/ directory.  This directory is included in the default command-search path of Mac OS X 10.5 (leopard), but not included in that of Mac OS X 10.4 (tiger).  You can check and modify your path as follows.

STEP 1 Open a terminal window (Finder → Applications → Utilities → Terminal).

STEP 2 Check whether mafft is already in your path by typing 'which mafft':

prompt$ which mafft
no mafft in /bin /sbin /usr/bin /usr/sbin  → Click here to show/hide STEP 3.

prompt$ which mafft
(Nothing returned)Click here to show/hide STEP 3.

prompt$ which mafft
/usr/local/bin/mafft → Nothing to do!

prompt$ which mafft
prompt$ rm /somewhere/else/mafftRe-install mafftReturn to STEP 2.
In the last case (ie. if you have installed mafft at a different directory than /usr/local/bin/), we recommend to use /usr/local/bin/mafft instead of the unusual installation (/somewhere/else/mafft) unless you have a special reason.  

See also here and here.