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This PR provides the base MrBayes integration, completing #195 for DNA/RNA analysis.

The code is not fully tested, and there may be some edge cases to be solved further, such as Mixture Models and Non-Time Reversible Models.

Current cases which have been tested:

  • Non-Partitioned Output + Importing into MrBayes
  • Partitioned Output + Importing into MrBayes
  • Merged Partitioned Output + Importing into MrBayes
  • Mapping of +R models
  • Mapping of custom defined models (e.g. 010010 to nst=2)

Base Logic:

  • MrBayes files will be outputted when the user provides the -mset mrbayes, or adds the -mrbayes flag
  • Two MrBayes files will be exported: one with parameters optimized from IQTree (.mr_bayes_model.nex), and one without (.mr_bayes_scheme.nex)
  • MrBayes files will be outputted on partitioned and non-partitioned runs

Support is planned for Protein, Codon, Binary and Morphological Data.

@thomaskf thomaskf merged commit 777c238 into iqtree:MrBayesSupport Jul 4, 2024
@IntegerLimit IntegerLimit deleted the mrbayes-block-support branch July 4, 2024 07:15
IntegerLimit added a commit to IntegerLimit/iqtree2 that referenced this pull request Jul 8, 2024
* Support Exporting DNA/RNA Analysis to MrBayes Block Files

* Fix Formatting Issues

* Move Functions to Supplementary, Fix +R Remapping
IntegerLimit added a commit to IntegerLimit/iqtree2 that referenced this pull request Apr 23, 2025
* Support Exporting DNA/RNA Analysis to MrBayes Block Files

* Fix Formatting Issues

* Move Functions to Supplementary, Fix +R Remapping
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2 participants