Automated generation of BEAST XML files, with a focus on dating phylogenies of HIV sequences
The easiest way to install rBEAST
is to use the devtools
package:
# install.packages("devtools")
library(devtools)
install_github("olli0601/rBEAST")
beastxml.multilocus.hky.fixed.tree
and beastxml.multilocus.codon.gtr
.beast.pool.clusters
. This can be useful if mixing is poor on a BEAST run comprising all taxa. In this case, sequences of the same cluster can be pooled into smaller taxon sets with this function.beastxml.from.template
. This can be useful to generate multiple XML files, each for a pool of sequences, when a (simple) template file is already at hand. This function can add monophyly constraints and logged tmrca statistics for each cluster. In this case, it may be necessary to specify a starting tree with the function beast.get.startingtree
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