View source: R/TreeQuartetDist.R
QDC | R Documentation |
Compute the Quartet Distance Consensus \insertCiteRho19MSCquartets estimate of an unrooted topological species tree from gene tree data.
QDC( genetreedata, taxanames = NULL, method = fastme.bal, omit = FALSE, metric = FALSE )
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 |
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.
an unrooted tree of type phylo
Rho19MSCquartets
quartetTable
,
quartetTableResolved
,
quartetTableDominant
,
quartetDist
,
QDS
,
WQDC
,
WQDCrecursive
estimateEdgeLengths
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)
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