Mothur executable in Windows



I’m new to bioinformatics and am trying to learn how to use mothur. I installed it in my Windows PC and is now trying to input data files (from sequencing). I followed the MiSeq SOP, manuals and tutorials, but I keep getting errors such as files/directory cannot be found or not writable. I am kind of lost how to get the directory and input files together, whether in the command line or interactive mode. Please help! Thank you very much.


Hi and welcome to using mothur!

You will need to use your command prompt to navigate to the directory that contains mothur and your data. I’d suggest dumping all of the files in the mothur directory and all of the reference files and sequences files in the same directory - there should not be any directories in your directory. Once you use cd to move to that directory, you should be able to type mothur.exe at the command prompt and have mothur start for you.



It worked! Thank you very much!