While using progressiveMauve (build date 13 February 2015), I noticed that when I run mauve twice with the same fasta file path arguments, but with these fasta files having a bit different contents on the second run, mauve gave wrong results on the second run.
When I removed the .sslist file that mauve created on the first run, the second run gave good results.
So my guess is that I got wrong results on the second run (in case I didn't remove the .sslist file) because mauve saw the .sslist file that was generated on the first run and skipped generating it and just used it, even though it did not fit the new sequences, leading to wrong results.
(My workaround for this is to simply always delete the .sslist file (if it exists) before running progressiveMauve)
While using progressiveMauve (build date 13 February 2015), I noticed that when I run mauve twice with the same fasta file path arguments, but with these fasta files having a bit different contents on the second run, mauve gave wrong results on the second run.
When I removed the .sslist file that mauve created on the first run, the second run gave good results.
So my guess is that I got wrong results on the second run (in case I didn't remove the .sslist file) because mauve saw the .sslist file that was generated on the first run and skipped generating it and just used it, even though it did not fit the new sequences, leading to wrong results.
(My workaround for this is to simply always delete the .sslist file (if it exists) before running progressiveMauve)