Comments (1)
Yes, all sites are included for tree inference. Even the constant sites are "informative" for maximum likelihood, as they help to estimate branch lengths properly.
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Related Issues (20)
- Help with IQ-TREE HOT 3
- Constraint not compatible with ModelFinder? HOT 5
- Segmentation fault when trying to use lds2 with predefined substitution rates HOT 2
- CMake deprecation warning: Compatibility with CMake < 3.5 will be removed from a future version of CMake.
- Build fails on ARM Mac (macOS 14) with `Error at CMakeLists.txt:701 (add_subdirectory)` HOT 4
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- Cannot find exact build setup used to make the release binaries HOT 1
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- Compilation failure with GCC 12 HOT 8
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- A possible bug? HOT 8
- Enhancement request: Implement +ASC option to speed up MixtureFinder searches on supermatrices lacking constant sites HOT 3
- SIGNAL SEGMENTATION FAULT HOT 2
- Feature request: Generate MrBayes block from IQ-TREE HOT 4
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- Process stuck in INITIALIZING CANDIDATE TREE SET HOT 3
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