Repeatscout installation problem
If you're in the RepeatScout directory you need to execute the Perl script with a ./ prefix, like so.

cat od_1000_repeats.fa | ./filter-stage-1.prl &gt; od_1000_repeats_filt1.fa


If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your $PATH environmental variable.

These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.