Cannot execute file 32 bit Ubuntu 10.10

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:

  1. Download the source file version of mothur.
  2. Unzip the source folder and open the file called makefile.
  3. Take a look at the makefile options, and edit the makefile to meet your needs.
  4. 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.