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babette is an R package that combines:

• beautier creates BEAST2 input (.xml) files.
• beastier runs BEAST2
• mauricer install BEAST2 packages
• tracerer parses BEAST2 output (.log, .trees, etc) files.

Related R packages:

• lumier: Shiny app to help create the function call needed

See:

• lumier: R Shiny app to help create the R function call needed
• examples
• article, in 'Methods in Ecology and Evolution'
• blog post in Methods.Blog
• pre-print article, in bioRxiv
• 'babette' YouTube channel

See doc/install.md (or just click here)

See FAQ.

babette cannot do everything BEAUti and BEAST2 and Tracer can.

See beautier for missing features in creating a BEAST2 input (.xml) file.

See beastier for missing features in running BEAST2

See mauricer for missing features in installing BEAST2 packages.

See tracerer for missing features in parsing BEAST2 output (.log, .trees, etc) files.

See CONTRIBUTING, at Submitting use cases

See CONTRIBUTING, at 'Submitting code'

See CONTRIBUTING, at 'Submitting bugs'

Sure, just add an Issue. Or send an email.

Package
beautier
beastier
mauricer
phangorn		.
tracerer

Package
lumier

• BEAST2 GitHub

Article about babette:

• Bilderbeek, Richel JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032

@article{bilderbeek2018babette,
  title={babette: BEAUti 2, BEAST 2 and Tracer for R},
  author={Bilderbeek, Richèl JC and Etienne, Rampal S},
  journal={Methods in Ecology and Evolution},
  year={2018},
  publisher={Wiley Online Library}
}

FASTA files anthus_aco.fas and anthus_nd2.fas from:

• Van Els, Paul, and Heraldo V. Norambuena. "A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data." Ibis.