Data location & readline

Hi, I’m pretty new at all this, however I got the mothur running! I’m using Ubuntu.
1st question:
Is it possible to have the input and output files saved somewhere else than the programm folder? If not, it gets too stuffed and files get mixed.
2nd question:
I think I still have problems with the Readline Libraries or something, because whenever I want to use the arrows of my keyboard, strange symbols show up instead of scrolling the commands I entered before or moving through the line I wrote.
Thanks a lot!

  1. You can set the input and output file locations using the set.dir command,
  2. Are you using the mothur executable with readline, or did you build your own version of mothur from source? If you build from source, be sure to set the USEREADLINE=yes in the makefile.