Core Development: Vision, Scope and Requirements


To provide tools for computational science that are

  • easy to use, that is, well documented, have intuitive user interfaces with small learning curve.
  • open access, that is, open source, open xml format, facilitating reproducibility of results, runs on many platforms.
  • easy to extend, by having extensibility in design and small learning curve on the basic API.


Efficient testing of probabilistic hypotheses for sequence data analysis involving tree models.


To achieve the above, the following needs to be implemented:

  1. Data Format Standardisation & Validation Framework
  2. Class/Object to Data I/O mapping framework
  3. Common input language definition
  4. Document code/internals to enable auto-generation of API
  5. Implement auto-citation generator, methods section
  6. Refactor Core – sub/coa, related Junit test. One substitution model hierarchy, One coalescent likelihood et cetera
  7. multicoring/parallelisation – Investigate best approach (research)
  8. migrate to java 1.6
  9. general datatypes/sub models in BEAUTi
  10. implement plugin framework, associated doc for developer, and related test
  11. Implement “general” datatype in BEAST
  12. new datatypes – Microsatellites, SNPS
  13. better prior selection
  14. templates for standard analyses
  15. visualisations – geographical
  16. visualisations – posterior-prior
  17. visualisations – species-tree.
  18. BEAST book
  19. Unified IO Review
  20. Beauti and Beast common XML format, Simple XML format for end user,
  21. Unified Logic Layer – parameter object
  22. checkpointing

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Bayesian evolutionary analysis by sampling trees