Hello,
I was wondering it would be possible to update the check orient parameter on the webpage to let users know that if set to true (the current default) it seems to remove the gaps when it checks the reverse orientation (when the fasta provided is an alignment).
The removal of gaps might be an intended behavior but it would be helpful to highlight in that parameters information section (especially since it defaults to true and can result in the output file having sequences with different lengths when you expect it to be an alignment file).
Thanks
Jacob Nearing