WQDS: Compute the Weighted Quartet Distance Supertree

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

Compute the Weighted Quartet Distance Supertree

Description

Apply the Weighted Quartet Distance Supertree method of \insertCiteYR19;textualMSCquartets to a collection of quartets on n taxa together with internal quartet branch lengths, specified by a table.

Usage

WQDS(dqt, method = fastme.bal)

Arguments

dqt	an (n choose 4) x n+1) matrix of form output by quartetTableDominant
method	a distance-based tree building function (e.g., fastme.bal, NJ, etc.)

Details

This function is a wrapper which runs quartetWeightedDist, builds a tree, and then adjusts edge lengths with WQDSAdjustLengths.

Value

an unrooted metric tree, of type phylo

References

\insertRef

YR19MSCquartets

See Also

quartetTableDominant, quartetWeightedDist, WQDSAdjustLengths, WQDC, WQDCrecursive, QDS

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")
tree=WQDS(DQT)
write.tree(tree)
plot(tree)

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