QDC {MSCquartets} | R Documentation |
Compute Quartet Distance Consensus tree from gene tree data
Description
Compute the Quartet Distance Consensus (Rhodes 2020) estimate of an unrooted topological species tree from gene tree data.
Usage
QDC(
genetreedata,
taxanames = NULL,
method = fastme.bal,
omit = FALSE,
metric = FALSE
)
Arguments
genetreedata |
gene tree data that may be supplied in any of 3 forms:
|
taxanames |
if |
method |
a distance-based tree building function, such as |
omit |
|
metric |
if |
Details
This function is a wrapper which performs the steps of reading in a collection of gene trees, tallying quartets, computing the quartet distance between taxa, building a tree which consistently estimates the unrooted species tree topology under the MSC, and then possibly estimating edge lengths using the "simpleML" method.
Value
an unrooted tree of type phylo
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
quartetTable
,
quartetTableResolved
,
quartetTableDominant
,
quartetDist
,
QDS
,
WQDC
,
WQDCrecursive
estimateEdgeLengths
Examples
gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=taxonNames(gtrees)
stree=QDC(gtrees,tnames[1:6])
write.tree(stree)
plot(stree)
streeMetric=QDC(gtrees, tnames[1:6],metric=TRUE)
write.tree(streeMetric)
plot(streeMetric)