MixtureFinder update#47

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thomaskf wants to merge 36 commits intoiqtree:masterfrom

thomaskf:mixFinder_update

Commits on Mar 4, 2025

allow mAIC calculation for 0 or 1 "overlapping" sequences.
HuaiyanRen
committed

Commits on Mar 7, 2025

allow mAIC calculation for 2 "overlapping" sequences.
HuaiyanRen
committed

Commits on Mar 19, 2025

method: add one gappy sequence for "2-overlapping" cases.
HuaiyanRen
committed
fix bugs for old method of "2-overlapping" cases. Although we don't use is now.
HuaiyanRen
committed

Commits on Mar 21, 2025

Fix protein ambiguous preblem for mAIC. Only compute mAIC for DNA and protein.
HuaiyanRen
committed

Commits on Mar 26, 2025

Allow mAIC calculation for binary and codon data. Make mAIC calculation works for non-reversible models
HuaiyanRen
committed

Commits on May 12, 2025

Commits on May 14, 2025

update the checkpoint file to keep the model parameters of the best mixture model
thomaskf
committed

Commits on May 20, 2025

Fixed the issue in modelfinder
thomaskf
committed

Commits on May 22, 2025

Commits on May 26, 2025

Fix the issue for using mixtureFinder on alignment with single partition
thomaskf
committed

Commits on Jun 12, 2025

Remove the increase of the maximum number of iterations for mixture model
thomaskf
committed

Commits on Jun 13, 2025

Fixed the different RHAS parameters and branch lengths between the MixFinder and the initial values after MixFinder
thomaskf
committed

Commits on Jun 18, 2025