quartetWeightedDist: Compute the Weighted Quartet Distance between taxa

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Compute the Weighted Quartet Distance between taxa

Description

Compute the Weighted Quartet Distance between taxa of \insertCiteYR19;textualMSCquartets 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

\insertRef

YR19MSCquartets

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)

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.