quartetWeightedDist: Compute the Weighted Quartet Distance between taxa

Description Usage Arguments Value References See Also Examples

View source: R/TreeQuartetDist.R

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

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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

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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 Jan. 8, 2021, 2:10 a.m.