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Commits on Jul 11, 2024

• Fixed the issue when using linked exchangeabilities under the mixture of protein + FO model.

  thomaskf

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Commits on Jul 5, 2024

• Fixed #261 issue of init model name that has to be in all caps for linked exchangeabilities

  thomaskf

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Commits on Jun 23, 2024

• for Modelfinder always initialise +R[k+1] from +R[k] and repeatedly optimise with last weight halving towards 0 to achieve good likelihood

  bqminh

  committed
  bf167a0

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• make code compiled with C++17, change throw() to noexcept(false)

  bqminh

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Commits on Jun 22, 2024

• Fix bug restoring +R[k] from +R[k-1] and also change the restoring strategy

  bqminh

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  8bf737e

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• Initialise RateFree from estimated alpha instead of alpha 1.0

  bqminh

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Commits on Jun 12, 2024

• Revert the fix for the issue happened when performing ModelFinder on Q-Mixtures with same number of classes.

  thomaskf

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Commits on May 27, 2024

• Don't export the freq strings for the UNREST model

  trongnhanuit

  committed
  ae59775

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• Bug fixed: fix the state freqs from the user-defined model parameters for UNREST model

  trongnhanuit

  committed
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Commits on May 7, 2024

• revert initialisation in modelunrest.cpp

  bqminh

  authored
  ca6f98b

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• Merge branch 'master' into master

  bqminh

  authored
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Commits on Apr 8, 2024

• Remove the redundant variable.

  thomaskf

  committed
  d400e9a

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• Fixed the model dimension for linked-GTR model

  thomaskf

  committed
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Commits on Apr 5, 2024

• Fixed the incorrect parameter number when substitution matrix is fixed under --link-exchange-rate option

  thomaskf

  committed
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Commits on Apr 4, 2024

• Revert "fixed the m3 openmp dynamic scheduling issue"

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  thomaskf

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Commits on Apr 1, 2024

• fixed the m3 openmp dynamic scheduling issue

  thomaskf

  committed
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Commits on Mar 23, 2024

• remove the matrices ELM50 and MXM

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  thomaskf

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Commits on Mar 21, 2024

• Merge branch 'master' into opt_mix_model

  thomaskf

  committed
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• To change the optimization workflow same as Hector's for linked-substitution model

  thomaskf

  committed
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Commits on Mar 18, 2024

• print out the linked rate matrix to iqtree file

  thomaskf

  committed
  9d020df

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• fix the issues of optimising a linked substitution model

  thomaskf

  committed
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Commits on Feb 2, 2024

• Update the method 1 for initialization of freq vector for model mixture.

  thomaskf

  committed
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Commits on Jan 31, 2024

• Merge branch 'opt_mix_model' of https://github.com/iqtree/iqtree2 into opt_mix_model

  thomaskf

  committed
  da167ff

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• implemented different freq init methods

  thomaskf

  committed
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Commits on Jan 23, 2024

• Update the options for MixtureFinder

  thomaskf

  committed
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Commits on Nov 6, 2023

• Allow to specify the optimisation algorithm for Q-Mixture model

  thomaskf

  committed
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Commits on Oct 23, 2023

• Fixed the issue happened when performing ModelFinder on Q-Mixtures with same number of classes.

  thomaskf

  committed
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Commits on Oct 19, 2023

• Issue fixed by changing the General HMM Model to General Reversible HMM model.

  thomaskf

  committed
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Commits on Oct 18, 2023

• Fixed a bug in TM method, and added another method of assigning the category to sites according to posterior probabilities.

  thomaskf

  committed
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Commits on Oct 16, 2023

• Site-Type dependent model -- hmmster{tm}

  thomaskf

  committed
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Commits on Sep 28, 2023

• Merge remote-tracking branch 'origin/tree-mix' into opt_mix_model

  thomaskf

  committed
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• Merge remote-tracking branch 'origin/gtr_optim' into opt_mix_model

  thomaskf

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Commits on Sep 8, 2023

• Support the model mixture with fixed rates and weights, together with tree mixture

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  thomaskf

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Commits on Jul 25, 2023

• Merge branch 'master' into tree-mix

  thomaskf

  committed
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Commits on Jul 13, 2023

• Merge branch 'master' into opt_mix_model

  thomaskf

  committed
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