What's Changed

• Marginal Akaike Information Criterion @HuaiyanRen, #78, #79, #90, #92, #95, #97, #112, #126
• Updated the IQTREE3's reference by @thomaskf in #159
• Fig a bug in MixtureFinder by @HuaiyanRen in #164
• Alignment refactoring and bug fixing by @StefanFlaumberg in #160
• update the IQ-TREE 3 reference in README by @trongnhanuit in #165
• Bugfix4 by @thomaskf in #167
• Update libomp.a built with older targets (10 and 11 rather than 26) by @trongnhanuit in #170
• Bug fix for PMSF+I combinations by @StefanFlaumberg in #168
• Fix EM mixture-frequency optimization by @thomaskf in #175
• Apply mAIC to PartitionFinder by @HuaiyanRen in #127
• Fix two bugs associated with the -mem option by @StefanFlaumberg in #173
• Updated multi-threading strategy by @thomaskf in #169
• Harden Windows x86-64 CI LLVM install against Chocolatey 504 timeouts by @bqminh with @Copilot in #177
• Mixlen refactoring: Make GHOST compatible with PMSF by @StefanFlaumberg in #174

New Contributors

• @bqminh with @Copilot made their first contribution in #177

Full Changelog: v3.1.2...v3.1.3

What's Changed

• Update CI to compare the new IQ-TREE 3 vs IQ-TREE 2 (rather than pre-defined fixed values) by @trongnhanuit in #147
• Integrate the latest CMAPLE API (v2) by @trongnhanuit in #146
• fix a bug: when +ASC model is applied by @HuaiyanRen in #149
• Codon Newton fix and switch to Clang and embedded OpenMP for Linux by @thomaskf in #158
• clamped_uint.cpp: Fix duplicate instantiation errors with Clang 21 by @Jehops in #155

New Contributors

• @Jehops made their first contribution in #155

Full Changelog: v3.1.1...v3.1.2

What's Changed

• Fix --scfl gap detection for models with rate heterogeneity by @roblanf in #142

New Contributors

• @roblanf made their first contribution in #142

Full Changelog: v3.1.0...v3.1.1

This version improves the stability and code quality of the software, including several bug fixes.

What's Changed

• Mix finder update by @thomaskf in #19
• Fixed the issue happened when user specifies the RHAS model for mixture finder by @thomaskf in #20
• Fixed the issue #18 regarding LG4X,LG4M by @thomaskf in #28
• Merge Mixfinder_update to Huaiyan's branch by @HuaiyanRen in #36
• Urgent fix for MCMCTree control file generation and Hessian calculation with ASC flag. by @piyumalanthony in #41
• The models added by --madd cannot be skipped. by @thomaskf in #42
• Mix finder update by @HuaiyanRen in #62
• Fix a bug where +FU are not allowed in mixture models by @HS6986 in #49
• Fix a bug where the state frequencies of morphological (multistate) models are not printed in the .iqtree file by @HS6986 in #50
• Fix issue when using LSD2 for phylogenetic dating. by @piyumalanthony in #64
• Bug fix: Wrong handling of site-specific state freqs in AliSim by @StefanFlaumberg in #66
• move the line "Optimizing NNI: done..." to the medium verbose mode by @thomaskf in #67
• Library for IQTREE3 by @thomaskf in #53
• Add testing to workflow by @thomaskf in #71
• Update sequence type detection function by @HuaiyanRen in #68
• Add option to fix branch lengths to those in the input tree when using fit_tree in libiqtree by @thomaskf in #93
• Bug fixed: automatically switch to using Parsimony (instead of PLL) to build start trees for very large alignments by @trongnhanuit in #81
• Bug fixed: delay deleting the "first_insertion" pointer to avoid crashing in partition simulation by @trongnhanuit in #88
• fix: handle taxa count divisible by 32 by @magnified103 in #76
• Add memory usage check to GitHub Actions workflow by @Hashara in #75
• Allow for single-state alignments and remove misleading warnings by @StefanFlaumberg in #73
• Support Exporting Model and Partition Selections to MrBayes by @IntegerLimit in #29
• Ali taba by @thomaskf in #83
• Extend MixtureFinder to codon, binary, multistate, (and amino acid) data by @HS6986 in #11
• Update AliSim API in piqtree by @trongnhanuit in #104
• Add support for passing command line options for IQTREE library by @thomaskf in #118
• add weighted perturbation by @taranehkhosrojerdi in #105
• Improve the optimization of rho (of the FunDi model) by @trongnhanuit in #115
• Update phylotesting.cpp by @etw35 in #119
• Updates to improve the Softwipe score by @trongnhanuit in #77

New Contributors

• @StefanFlaumberg made their first contribution in #66
• @magnified103 made their first contribution in #76
• @IntegerLimit made their first contribution in #29
• @taranehkhosrojerdi made their first contribution in #105
• @etw35 made their first contribution in #119

Full Changelog: v3.0.1...v3.1.0

What's Changed

• Fix the issue in the workflow for Mac Universal by @thomaskf in #9
• Naser-Khdour et al. (2024) -> Naser-Khdour et al. (2019) by @HS6986 in #10
• Urgent bug fix for the issues #15 and #16 by @thomaskf in #17
• Fixed the issue regarding the GHOST model with an option -nt AUTO by @thomaskf in #22
• Fix issue for MCMCTree dating when there is a leaf at first child of the super tree and Formatted code for Hessain calculation. by @piyumalanthony in #24
• Updated ci.yaml to fix the issue of the Linux Intel binary file compiled on Github. by @thomaskf in #23
• Generate a Linux universal version in Github Actions by @trongnhanuit in #25

New Contributors

• @HS6986 made their first contribution in #10
• @piyumalanthony made their first contribution in #24

Full Changelog: v3.0.0...v3.0.1

This is the pre-release of IQ-TREE version 3