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feature/modeltest #2

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christoph wants to merge 38 commits from feature/modeltest into dev
pull from: feature/modeltest
merge into: christoph:dev
Conversation 0 Commits 38 Files changed 22 +2204 -1425
christoph commented 2025-01-14 10:29:09 +01:00
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This reverts commit b2da3640
This will allow easy comparison of results against ModelTest-NG
This reverts commit a865f8e451.
Equal frequencies does not apply to AA models, omitting +F is the thing we want here (taking the fixed frequencies specified by the model).

TrN is an alias resolved to TN93 by libpll/coraxlib, so we should use the resolved name to make things more explicit.
The same thread now continually increases the freerate category count until the BIC score no longer improves.
Move debug output to LOG_DEBUG to tidy up logging output.
Print current partition and total number of partitions.
christoph force-pushed feature/modeltest from ff415ee41d to b5413d6cca 2025-04-29 10:34:39 +02:00 Compare 
Bug was introduced after refactoring the way results were organized.
It caused only the first n models to be considered for the
ranking, where n is the number of partitions in the dataset.

The XML output was not affected.
This value is also used by ModelTest-NG.
The best model according to BIC score will then be used in the
subsequent command.
Currently checkpointing is not supported.
Remove left-over debug statement

Do not update Partitioned MSA inside ModelTest class but in main source
file instead (Principle of least surprise)
The new implementation no longer requires that the increasing category
count of a freerate candidate model is computed by the same thread.
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