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Tweak NEWS.
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bredelings committed Oct 22, 2023
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Showing 1 changed file with 10 additions and 12 deletions.
22 changes: 10 additions & 12 deletions NEWS
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* 4.0-beta7 (unreleased)
- Bug fixes:
+ Allow estimating the alignment with a fixed topology.
- Don't crash trying NNI on fixed tree.
- Allow discovering a single partition by supplying alignment regs.
- realign_from_tips: don't modify the branch lengths if they are fixed.
- Fix -l tsv with -m Model.hs
- Haskell
+ Report ancestral sequences as AlignedCharacterData.
+ Allow simulating from ctmc_on_tree.
+ Add class Alignment for common methods between AlignmentOnTree and AlignedCharacterData.
- Fix default instances for type families.
- Refactor Tree class to add Graph and Forest
- Haskell
+ Ancestral sequences are now AlignedCharacterData.
+ Sampled/observed sequences are Unaligned/AlignedCharacterData depending on if alignment is fixed.
+ Can now simulate from ctmc_on_tree.
+ Common methods between AlignmentOnTree and AlignedCharacterData now in class Alignment.
- Refactor generic methods in Tree class into classes Graph and Forest.
- AlignmentOnTree: Only store sequence lengths for some nodes.
- Add some instances for Data.Map
- Replace Sequence with (,)
- Add AlignedCharacterData, UnalignedCharacterData, CharacterData.
- Stop using C++ alignment class when compressing sequence data.
- Make ctmc_on_tree operate on UnalignedCharacterData.
- Make ctmc_on_tree_fixed_A operate on AlignedCharacterData.
- Add some instances for Data.Map
- Machine:
- Don't crash trying NNI on fixed tree.
- Better error message if trying to read/modify a non-modifiable.
- Allow discovering a single partition by supplying alignment regs.
- realign_from_tips: don't modify the branch lengths if they are fixed.
- Add associated type DistProperties, and return it from observed.
- Add sampleWithProps -- hacky version.
- Synchronize property indices between between variable and fixed-A.
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