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.
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.