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MixtureFinder update #47

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  1. Fixed the issue in mixtureFinder, by updating the checkpoint records with the best model parameters.
  2. Extended the mixtureFinder for an alignment with single partition. Have been tested with the partition options -p, -q and -Q.

HuaiyanRen and others added 30 commits March 4, 2025 16:21
@HuaiyanRen
allow mAIC calculation for 0 or 1 "overlapping" sequences.
f2c802b
@HuaiyanRen
allow mAIC calculation for 2 "overlapping" sequences.
96d6b53
@HuaiyanRen
method: add one gappy sequence for "2-overlapping" cases.
7357f83
@HuaiyanRen
fix bugs for old method of "2-overlapping" cases. Although we don't u…
aa60951 
…se is now.
@HuaiyanRen
Fix protein ambiguous preblem for mAIC. Only compute mAIC for DNA and…
219fd3f 
… protein.
@HuaiyanRen
Allow mAIC calculation for binary and codon data. Make mAIC calculati…
687002e 
…on works for non-reversible models
@thomaskf
Allow to fix the parameters for RHAS when using mixture finder. Also …
13b6892 
…allow both options: MIX+MF and MF+MIX
@thomaskf
Merge pull request iqtree#19 from thomaskf/mixFinder_update
81f4e7a 
Allow to fix the parameters for RHAS when using mixture finder.
Allow all these options: MIX+MF, MIX+MFP, MF+MIX, MFP+MIX -- to run the mixture finder
@thomaskf
Fixed the issue happened when user specifies the RHAS model when runn…
4710559 
…ing mixture finder.

Another option: -optfromgiven
The RHAS model will still be optimized according to the initial values same as the input parameters.
@thomaskf
Merge pull request iqtree#20 from thomaskf/mixFinder_update
dd0c411 
Fixed the issue happened when user specifies the RHAS model for mixture finder
@thomaskf
Merge branch 'master' into mixFinder_update
f262dbd
@HuaiyanRen
Merge branch 'master' into huaiyan
53ec25a
@thomaskf
Allow the option -m MIX+MF, MIX+MFP, MF+MIX, MFP+MIX to run MixtureFi…
988531d 
…nder
@thomaskf
Allow mixtureFinder on an alignment with a single partition
61342be
@thomaskf
Fixed the double commas inside the best_model.nex file
016a6b8
@thomaskf
Set the best model reported by mixturefinder to the first partition
0442a7a
@thomaskf
Save the model checkpoint to the file when mixtureFinder finishes
0ec0308
@thomaskf
Update mixtureFinder for alignment with single partition
d4aebb4
@HuaiyanRen
Merge remote-tracking branch 'origin/mixFinder_update' into mixFinder…
17eecd6 
…_update

# Conflicts:
#	main/phylotesting.cpp
@HuaiyanRen
report the mixture model in single partition in mixture model format.
e0e397c
@thomaskf
Fixed the issue of using these models LG4X,LG4M in -madd
98779b8
@HuaiyanRen
report the mixture model in only in single-partition alignment in mix…
d29ff88 
…ture model format.
@thomaskf
Copy the resulting final tree to the first partition for mixfinder wi…
64423b1 
…th single partition
@thomaskf
update the checkpoint file to keep the model parameters of the best m…
1e073ec 
…ixture model
@HuaiyanRen
Merge branch 'huaiyan' into mixFinder_update
0a9f5a5
@HuaiyanRen
report the mixture model in only in single-partition alignment STILL …
c6b25ab 
…in partition model format.
@thomaskf
introduce an option -mfopt to further optimise nucl/aa frequencies in…
66c5278 
… mixture model
@thomaskf
Add an option --writefreqchkpt to force writing nucl/aa freq to check…
6fc4e70 
…point file
@thomaskf
Fixed the issue in modelfinder
86c8cab
@thomaskf
Revert "Add an option --writefreqchkpt to force writing nucl/aa freq …
781d602 
…to checkpoint file"

This reverts commit 6fc4e70.
@trongnhanuit trongnhanuit mentioned this pull request Jun 4, 2025
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2 participants
@thomaskf @HuaiyanRen