Showing 5 of total 5 results (show query)
ropensci
babette:Control 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.
Maintained by Richèl J.C. Bilderbeek. Last updated 2 days ago.
bayesian-inferencebeast2phylogeneticsopenjdk
45 stars 8.55 score 53 scripts 1 dependentsropensci
beastier:Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
Maintained by Richèl J.C. Bilderbeek. Last updated 1 months ago.
bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk
11 stars 7.87 score 47 scripts 4 dependentsropensci
mauricer:Work with 'BEAST2' Packages
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2' (<https://www.beast2.org>), which, among others, allows one to install 'BEAST2' package. This package allows to work with 'BEAST2' packages from 'R'.
Maintained by Richèl J.C. Bilderbeek. Last updated 7 months ago.
3 stars 5.56 score 10 scripts 2 dependentsropensci
mcbette:Model Comparison Using 'babette'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (<https://github.com/ropensci/babette/>).
Maintained by Richèl J.C. Bilderbeek. Last updated 8 months ago.
7 stars 5.50 score 18 scripts
thijsjanzen
nodeSub:Simulate DNA Alignments Using Node Substitutions
Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
Maintained by Thijs Janzen. Last updated 1 years ago.
1 stars 2.70 score 3 scripts