The make command is not working because you downloaded the executable and so there is no makefile. It seems the executable is not working for you. I would do the following:
- Download the source file version of mothur.
- Unzip the source folder and open the file called makefile.
- Take a look at the makefile options, and edit the makefile to meet your needs. http://www.mothur.org/wiki/Makefile_options
- Now the make command should work and build the mothur executable for you.
If any of this is unclear, feel free to ask more questions, I am happy to help.
-Sarah