quartetDist: Compute quartet distance between taxa

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

Compute quartet distance between taxa

Description

Compute the Quartet Distance of \insertCiteRho19;textualMSCquartets from a table specifying a collection of quartets on n taxa.

Usage

quartetDist(dqt)

Arguments

dqt	an (n choose 4) x n (or n+1) matrix of form output by quartetTableDominant; (Note: If present, the n+1th column of dqt is ignored.)

Value

a pairwise distance matrix on n taxa

References

\insertRef

Rho19MSCquartets

See Also

quartetTableDominant, QDS, QDC, 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)
Dist=quartetDist(DQT)
tree=NJ(Dist)
write.tree(tree)
plot(tree)

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