Version 2.4.0

This release includes a major bug fix of AliSim (Bug ID #333). This bug occurred due to the use of identical random seed numbers for generating the root sequence and simulating its first descendant sequence, which resulted in identical sequences at the root and its first child node.

For more detailed information about the bug, its effects, the impacted release versions, and a list of papers that might be affected, please refer to our comprehensive bug report.

We apologize for any inconvenience this bug may have caused.

Version 2.3.6

This release supports the new Apple Mx (ARM) chips, Linux (ARM) chips, and a series of mixture models for phylogenomics.

Major Features:

• Ability to link exchangeability rates for (amino-acid) profile mixture models, with a nexus file outputted for the estimated substitution matrix. The options --link-exchange and --init-exchange are now available.
• Mixture across sites and trees, MAST model.
• MixtureFinder, to automatically select DNA mixture models.
• Support for the new Apple Mx chips (Use clang17 or above for compilation)
• Support for Linux ARM (Use clang14 or above to compile the source codes)

Several Bug Fixes and Enhancements:

• Fixed the #255 issue -- Infinite loop while using BNNI under PMSF model
• Fixed the #261 issue -- Init linked exchangeabilities model name no need to be in all caps
• Fixed the #272 issue -- Bug in writing best_model.nex file
• Fixed the GTRpmix file format
• Added a user warning when the induced root is not found in gCF
• Added the supported platforms shield to readme

Version 2.3.5

This release supports the new Apple Mx (ARM) chips, Linux (ARM) chips, and a series of mixture models for phylogenomics.

Major Features:

• Ability to link exchangeability rates for (amino-acid) profile mixture models, with a nexus file outputted for the estimated substitution matrix. The options --link-exchange and --init-exchange are now available.
• Mixture across sites and trees, MAST model.
• MixtureFinder, to automatically select DNA mixture models.
• Support for the new Apple Mx chips (Use clang17 or above for compilation)
• Support for Linux ARM (Use clang14 or above to compile the source codes)
• Fixed the #179 issue when running with the constraint tree feature, the option --keep-ident is now forced to "on"
• Several bug fixes to improve software stability.

Version 2.3.5.cmaple

This release incorporates a couple of bug fixes.

Major Features:

• Fixed the #156 issue when generating the AliSim command.
• Fixed the #160 issue when simulating alignments with the UNREST model.

Version 2.3.4

This release supports the new Apple Mx (ARM) chips, Linux (ARM) chips, and a series of mixture models for phylogenomics.

Major Features:

• Fixed the #180 issue when running with the constraint tree feature and bootstrapping, and the input constraint-tree file contains internal node names
• Support for the new Apple Mx chips (Use clang17 or above for compilation)
• Support for Linux ARM (Use clang14 or above to compile the source codes)
• Mixture across sites and trees, MAST model.
• A new method, MixtureFinder, to automatically select DNA mixture models.
• Ability to link exchangeability rates for (amino-acid) profile mixture models, with a nexus file outputted for the estimated substitution matrix.
• Several bug fixes to improve software stability.

Version 2.3.4.cmaple

This release integrates the (C)MAPLE algorithm, which allows IQ-TREE to reconstruct a tree from a large-scale pathogen alignment. For usage instructions, please see HERE.

Version 2.3.3

This release supports the new Apple Mx (ARM) chips, Linux (ARM) chips, and a series of mixture models for phylogenomics.

Major Features:

• To speed up the analysis, the ModelFinder default algorithm has been changed to the Fast Relaxed Algorithm.
• #166 issue regarding the constraint tree feature incompatible with ModelFinder has been fixed.
• Support for the new Apple Mx chips (Use clang17 or above for compilation)
• Support for Linux ARM (Use clang14 or above to compile the source codes)
• Mixture across sites and trees, MAST model.
• A new method MixtureFinder to automatically select DNA mixture models.
• Ability to link exchangeability rates for (amino-acid) profile mixture models, with a nexus file outputted for the estimated substitution matrix.
• Several bug fixes to improve software stability.

Version 2.3.2

This release supports the new Apple Mx (ARM) chips, Linux (ARM) chips, and a series of mixture models for phylogenomics.

Major Features:

• Support for the new Apple Mx chips (Use clang17 or above for compilation)
• Support for Linux ARM (Use clang14 or above to compile the source codes)
• Mixture across sites and trees, MAST model.
• A new method MixtureFinder to automatically select DNA mixture models.
• Ability to link exchangeability rates for (amino-acid) profile mixture models, with a nexus file outputted for the estimated substitution matrix.
• Several bug fixes to improve software stability.

Version 2.3.1

This is a major release which now supports for the new Apple Mx (ARM) chips and a series of mixture models for phylogenomics.

Major Features:

• Support for the new Apple Mx chips.
• Mixture across sites and trees, MAST model.
• A new method MixtureFinder to automatically select DNA mixture models.
• Ability to link exchangeability rates for (amino-acid) profile mixture models.
• Several bug fixes to improve software stability.

Version 2.3.0

Updated version of multi-tree mixture model (i.e. Mixture Across Sites and Trees (MAST) model).

The manuscript is available here

User manual for the MAST model is available here