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babette is the wrapper around beautier, beastier and tracerer (#16)
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Co-authored-by: Richel Bilderbeek <richelbilderbeek@users.noreply.github.com>
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richelbilderbeek and richelbilderbeek authored Jun 28, 2024
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Expand Up @@ -279,7 +279,7 @@ See the `r view("Epidemiology")` task view for details about packages useful for
- `r pkg("ape")` can call [PhyML](http://www.atgc-montpellier.fr/phyml/), [Clustal](http://www.clustal.org/), [T-Coffee](https://tcoffee.crg.eu/), and [Muscle](https://www.drive5.com/muscle/) through various functions.
- `r pkg("geiger")` can call PATHd8 through its congruify function.
- `r pkg("ips")` wraps several phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states, including MrBayes, Beast, [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/), [PartitionFinder](https://www.robertlanfear.com/partitionfinder/), and [MAFFT](https://mafft.cbrc.jp/alignment/software/), allowing their easy use from within R.
- `r pkg("beastier")` can call [BEAST2](https://www.beast2.org/) to perform phylogenetic analyses, `r pkg("beautier")` can generate XML input files for BEAST2 (like [BEAUti](https://www.beast2.org/beauti/)), and `r pkg("tracerer")` can be used to parse and analyze BEAST2 output files (like [Tracer](https://github.com/beast-dev/tracer/)). `r pkg("beastier")` is a wrapper for all of these packages.
- `r pkg("beastier")` can call [BEAST2](https://www.beast2.org/) to perform phylogenetic analyses, `r pkg("beautier")` can generate XML input files for BEAST2 (like [BEAUti](https://www.beast2.org/beauti/)), and `r pkg("tracerer")` can be used to parse and analyze BEAST2 output files (like [Tracer](https://github.com/beast-dev/tracer/)). `r pkg("babette")` is a wrapper for all of these packages.
- `r github("liamrevell/Rphylip")` wraps [PHYLIP](http://evolution.genetics.washington.edu/phylip.html) , a broad variety of programs for tree inference under parsimony, likelihood, and distance, bootstrapping, character evolution, and more.
- `r pkg("BoSSA")` can use information from various tools to place a query sequence into a reference tree.
- `r pkg("BAMMtools")` is an interface to the BAMM program to allow visualization of rate shifts, comparison of diversification models, and other functions.
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