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AliSim 3Di/TEA: note auto-classifier is less reliable on simulated data; specify -st
AliSim 3Di/TEA: recommend ASR root to capture site dependence
Document 3Di and TEA structural-alphabet models
Clarify branch-specific rate heterogeneity models
Update 2.4.0 as the recommendation version for AliSim
change all iqtree2 to iqtree3 (except "for older versions")
Updated AliSim (markdown)
add double quotes to avoid errors due to curly bracket parsing - converting A{1,2} into A1 A2
update citation for AliSim doc
Update ALiSim-HPC citation
Clarify the branch-specific model
add version for --mutation feature
revise mutation rule
Minor changes in AliSim
Add option to set the starting index
Update AliSim - Pre-define mutations
Use a comma (instead of a forward slash) as the separator for predefining a list of mutations
Add urls
Support predefined mutations in AliSim
Change -af to --out-format
change diff to maple
Add MAPLE format
Update AliSim paper(s)
Introduce --no-merge option in AliSim user manual
Minor updates in AliSim user manual
Add user manual for AliSim-HPC
Introduce option --single-output to output all alignments into a single file
change option --no-unaligned
Merge branch 'master' of https://github.com/iqtree/iqtree2.wiki