MSCquartets: QDS – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

QDS

Compute Quartet Distance Supertree

Description

Apply the Quartet Distance Supertree method of Rhodes (2020) to a table specifying a collection of quartets on n taxa.

Usage

QDS(dqt, method = fastme.bal)

Arguments

`dqt`	an (`n` choose 4) x `n` (or `n+1`) matrix of form output by `quartetTableDominant`; (Note: If present, the `n+1`th column of `dqt` is ignored)
`method`	tree building function (e.g., fastme.bal, nj)

Details

This function is a wrapper which runs quartetDist and then builds a tree.

Value

an unrooted metric tree of type phylo. Edge lengths are not in interpretable units

References

Rhodes JA (2020). “Topological metrizations of trees, and new quartet methods of tree inference.” IEEE/ACM Trans. Comput. Biol. Bioinform., 17(6), 2107–2118. doi: 10.1109/TCBB.2019.2917204, https://doi.org/10.1109/TCBB.2019.2917204.

Examples

gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=taxonNames(gtrees)
QT=quartetTable(gtrees,tnames[1:6])
RQT=quartetTableResolved(QT)
DQT=quartetTableDominant(RQT)
tree=QDS(DQT)
write.tree(tree)
plot(tree)

MSCquartets

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

v1.1.0

MIT + file LICENSE

Authors

Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], John Rhodes [aut, cre] (<https://orcid.org/0000-0001-9921-1091>)

Initial release

QDS