quartetWeightedDist {MSCquartets}

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.

See Also

quartetTableDominant, WQDSAdjustLengths, WQDS, WQDC, WQDCrecursive, quartetWeightedDist

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)