simulate alignment from the 2nd lphy script

[walterxie]

~~ Select the alignment given ID (e.g. random variable name) in the LPhy script. ~~

Update to use the 2nd lphy script to simulate data

[alexeid]

remember that it is possible in general to have more than one alignment involved in a BEAST analysis (like multiple partitions, or one morphology alignment and one molecular alignment, or combinations of these).

On 9/12/2022, at 11:28 AM, Walter @.***> wrote:

Select the alignment given ID (e.g. random variable name) in the LPhy script.

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[walterxie]

I had this caution in my mind, there is a validation to check if there are any multiple alignments using this feature, if yes, then throw UnsupportedException. I will improve it after the required cancer data analyses are completed.

[walterxie]

TODO:

1. Use the simulated alignment from the 2nd lphy script to replace the alignment in the main script, given ID. So the main script can apply the diff model with the simulation model to the simulated data.
2. Handle the multiple alignments.