Compute quartet distance between taxa
Compute the Quartet Distance of Rhodes (2020) from a table specifying a collection of quartets on
n taxa.
quartetDist(dqt)
dqt |
an ( |
a pairwise distance matrix on n taxa
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, https://doi.org/10.1109/TCBB.2019.2917204.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.