Mothur :: interactive command

Mothur is downloaded and stored in a file
/path/to/Mothur/

After, 'make' the binary for calling mothur is in
/path/to/Mothur/Mothur.source/mothur

To execute this command from any folder, provide a soft link to the folder in /usr/local/bin/
$ ln -s /path/to/Mothur/Mothur-source/mothur mothur

To confirm the setup
$ which mothur
/usr/local/bin/mothur

mothur command can now be run from any folder.