QDS {MSCquartets}

Compute Quartet Distance Supertree

Description

Apply the Quartet Distance Supertree method of Rhodes (2020) 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

Rhodes JA (2020). “Topological metrizations of trees, and new quartet methods of tree inference.” IEEE/ACM Trans. Comput. Biol. Bioinform., 17(6), 2107-2118. doi:10.1109/TCBB.2019.2917204.

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)