William S. DeWitt

I am also not getting the pdf to update after recompiling. I have to close the file and reopen.

@allefeld Looks cool, although I'm finding the same issue on macOS Catalina: pdf refreshes in the Preview app after a new tex build, but does not reload in the pdfjs-viewer...

@allefeld Thanks! Indeed this seems related to the pdf recreation method. I am using SCons for TeX build, which by default deletes targets before rebuilding. This SCons behavior can be...

I am seeing larger parsimony forests with more jumbles, using the following commands. ```bash deduplicate example/150228_Clone_3-8.fasta --root GL > deduplicated.phylip mkconfig --jumble 10 deduplicated.phylip dnapars > dnapars.cfg dnapars < dnapars.cfg...

Ok I retried without `--quick` and found 263 trees with 1 jumble and with 2 jumbles (you found the same number using 10 or 100 jumbles). I'm not sure if...

Good point. Ok maybe we should ask Joe. Do you agree @matsen?