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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
add custom distribution file
update manual pdf front page
update AliSim doc version
Minor revised AliSim
Merge branch 'master' of https://github.com/iqtree/iqtree2.wiki # Fix Conflicts: # AliSim.md
Revised Command reference