Related Issues (20)
- Update documentation HOT 2
- Revise paper HOT 6
- Make `--states-present` default option for NEXUS output
- Add support for `--ascertainment` option HOT 4
- Add `--long-table` option for tabular output
- Fix github actions workflow for iqtree HOT 1
- Failure with no user-oriented error message HOT 10
- Should teiphy convert all variation units, including trivial ones?
- Add support for BEAST XML output HOT 73
- add tip date sampling for beast HOT 5
- Create directory for output if needed HOT 1
- Relative path to chron file for stemma output HOT 2
- Assignment of random starting rate parameter values, new prior distributions, and support for `--seed` option
- Add support for NEXUS-style CSV/Excel output HOT 1
- Change CSV outputs to include BOM HOT 1
- Use fixed origin for BEAST BDSKY model if tradition has a fixed composition date
- Change AncestralStateLogger to AncestralSequenceLogger in BEAST output
- Add option for choice of AncestralSequenceLogger or AncestralStateLogger for BEAST outputs
- Add support for time-dependent substitution models with EpochSubstitutionModel in BEAST outputs HOT 2
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