QDS: Compute Quartet Distance Supertree

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

Compute Quartet Distance Supertree

Description

Apply the Quartet Distance Supertree method of \insertCiteRho19;textualMSCquartets to a table specifying a collection of quartets on n taxa.

Usage

QDS(dqt, method = fastme.bal)

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)
method	tree building function (e.g., fastme.bal, nj)

Details

This function is a wrapper which runs quartetDist and then builds a tree.

Value

an unrooted metric tree of type phylo. Edge lengths are not in interpretable units

References

\insertRef

Rho19MSCquartets

See Also

quartetTableDominant, quartetDist, QDC, WQDS, WQDC, WQDCrecursive

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)
tree=QDS(DQT)
write.tree(tree)
plot(tree)

MSCquartets documentation built on Nov. 2, 2023, 5:32 p.m.