MSCquartets: WQDS – R documentation

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WQDS

Compute the Weighted Quartet Distance Supertree

Description

Apply the Weighted Quartet Distance Supertree method of Yourdkhani and Rhodes (2020) to a collection of quartets on n taxa together with internal quartet branch lengths, specified by a table.

Usage

WQDS(dqt, method = fastme.bal)

Arguments

`dqt`	an (`n` choose 4) x `n+1`) matrix of form output by `quartetTableDominant`
`method`	a distance-based tree building function (e.g., fastme.bal, NJ, etc.)

Details

This function is a wrapper which runs quartetWeightedDist, builds a tree, and then adjusts edge lengths with WQDSAdjustLengths.

Value

an unrooted metric tree, of type phylo

References

Yourdkhani S, Rhodes JA (2020). “Inferring metric trees from weighted quartets via an intertaxon distance.” Bul. Math. Biol., 82(97). doi: 10.1007/s11538-020-00773-4, https://doi.org/10.1007/s11538-020-00773-4.

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,bigweights= "finite")
tree=WQDS(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