MSCquartets: quartetWeightedDist – R documentation

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quartetWeightedDist

Compute the Weighted Quartet Distance between taxa

Description

Compute the Weighted Quartet Distance between taxa of Yourdkhani and Rhodes (2020) from a table specifying a collection of quartets on n taxa and the quartets' internal branch lengths.

Usage

quartetWeightedDist(dqt)

Arguments

dqt

an (n choose 4) x (n+1) matrix of the form output by quartetTableDominant

Value

a pairwise distance matrix on n taxa

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")
D=quartetWeightedDist(DQT)
tree=NJ(D)
stree=WQDSAdjustLengths(tree)
write.tree(stree)

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