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CompEvol / BeastFX

GUIs for BEAST using Java FX to make things more pretty.
GNU Lesser General Public License v2.1
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Bug fix and improvements for BeautiTabPane and BeautiDoc argument parsers #52

Closed tgvaughan closed 1 year ago

tgvaughan commented 1 year ago

Hi Remco, here is the bugfix I mentioned.

Also, I've snuck in a couple of additional command line arguments "-fasta_nucleotide" and "-fasta_aminoacid" which, like "-nex", let people supply an alignment on the command line. I find this incredibly helpful when developing beauti templates, as the File->Import alignment step can become very tedious.

If you don't like the look of the extra options, let me know and I'll remove them from the PR.

rbouckaert commented 1 year ago

Thanks for the bug fix, Tim! I missed that.

The -version_file interpretation should be the same for BEAST and BEAUti.

Adding loading of fasta files makes sense, so I happily included that.