Unlinked codons and state reconstruction in BEAUTi

[msuchard]

Originally reported on Google Code with ID 636

What steps will reproduce the problem?
1. Use BEAUTi to make an XML file with ancestral state reconstruction at all ancestors
(for the nucleotide sequence) with two codon position partitions.
2. Run it in BEAST.

What is the expected output? What do you see instead?

The error is "Object with idref=CP1.treeLikelihood has not been previously declared."
This is because the ancestralTreeLikelihood idrefs in the logTree block are to "CP1"
and "CP2" when they should be "CP1+2" and "CP3", as far as I can see.

Reported by mdhall272 on 2012-06-19 11:02:07

[msuchard]

Reported by mdhall272 on 2012-06-19 11:03:01

[msuchard]

Reported by rambaut on 2012-08-01 13:55:39

• Labels added: BEAUti, 1.7.2, Milestone-Release1.7.3

[msuchard]

Reported by rambaut on 2012-08-01 16:16:27

• Labels added: Milestone-Release1.7.4
• Labels removed: Milestone-Release1.7.3

[msuchard]

Reported by rambaut on 2012-08-02 14:17:58

• Labels added: Priority-High, Milestone-Release1.7.3
• Labels removed: Priority-Low, Milestone-Release1.7.4

[msuchard]

Reported by rambaut on 2012-08-03 14:55:04

• Status changed: Fixed