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beautier
is BEAUti
for R.
The purpose of beautier
is to create a valid BEAST2 XML input file from a n inference model. In this way, a scientific pipeline using BEAST2
can be fully scripted, instead of using BEAUti
’s GUI.
beautier
is part of the babette
package suite:
beautier
create a BEAST2 input (.xml
) file from an inference model.tiebeaur
creates an inference model from a BEAST2 input (.xml
) file ⚠️ experimental ⚠️
beastier
runs BEAST2tracerer
pastes BEAST2 output (.log
, .trees
, etc) files.mauricer
install BEAST2 packagesRelated R packages:
beautier_on_windows
: verifies beautier
builds on Windowslumier
: Shiny app to help create the function call neededSee examples.
beautier
can be installed:
master
branchdevelop
branchdevelop
branchFor the bleeding-edge version:
remotes::install_github("ropensci/beautier", ref = "develop")
This works, and the interface is unlikely to change.
beautier
cannot do everything BEAUti
can.
Here are some missing or (yet) unsupported features:
BEAUti
)See CONTRIBUTING, at Submitting use cases
See CONTRIBUTING, at ‘Submitting code’
See CONTRIBUTING, at ‘Submitting bugs’
Article about babette
:
babette
: BEAUti 2, BEAST 2 and Tracer for R.” Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032
FASTA files anthus_aco.fas
and anthus_nd2.fas
from:
FASTA file G_VII_pre2003_msa.fas
from: