[WIP: Implementation of a New Algorithm] Extension of MixtureFinder to morphological data#35

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HS6986 wants to merge 58 commits intoiqtree:masterfrom

HS6986:feature/HS6986/MorphMixtureFinder

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
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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 Apr 6, 2025

extend MixtureFinder to codon, binary, multistate, and amino acid data
HS6986
committed

Commits on Apr 8, 2025

fix frequency types
HS6986
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Commits on Apr 15, 2025

allow FU in mixture models
HS6986
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Commits on Apr 28, 2025

Commits on Apr 29, 2025

Commits on May 11, 2025

Commits on May 12, 2025

Commits on May 13, 2025

Implement a new MixtureFinder-like algorithm for selecting mixture models for morphological data, which has not yet been validated
HS6986
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Commits on May 14, 2025

update the checkpoint file to keep the model parameters of the best mixture model
thomaskf
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Commits on May 26, 2025

Merge remote-tracking branch 'upstream/master' into feature/HS6986/MorphMixtureFinder
HS6986
committed