I just started using the linnux version of mothur coming from the windows side and wanted to make sure it’s running properly. When I run the multiple processor command, it looks like it generates a set of temporary files (one for each processor I specify) and then recombines these files into one at the end. Is this how the multiple processor feature works? I’m only asking since the progress bar that displays the progress (while running an alignment or distance matrix with multiple processors) seems to jump occassionally. I’m just curious if everything is working as it should. I think it is since I’m getting similar results running test samples on each version, but if someone could confirm this I’d appreciate it.