MSCquartets: QDC – R documentation

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QDC

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: a character string giving the name of a file containing gene trees in Newick, a multiPhylo object containing gene trees, or a resolved quartet table, such as produced by `quartetTableResolved`
`taxanames`	if `genetreedata` is a file or a multiPhylo object, a vector of a subset of the taxa names on the gene trees to be analyzed, if `NULL` all taxa on the first gene tree are used; if `genetreedata` is a quartet table, this argument is ignored and all taxa in the table are used
`method`	a distance-based tree building function, such as `fastme.bal` or `nj`
`omit`	`TRUE` ignores unresolved quartets; `FALSE` treats them as 1/3 of each resolution; ignored if `genetreedata` is supplied as a quartet table
`metric`	if `FALSE` return topological tree; if `TRUE` return metric tree with internal edge lengths estimated by `estimateEdgeLengths` with `lambda=0`, and terminal branches of length 1

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, https://doi.org/10.1109/TCBB.2019.2917204.

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)

MSCquartets

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

v1.1.0

MIT + file LICENSE

Authors

Elizabeth Allman [aut], Hector Banos [aut], Jonathan Mitchell [aut], John Rhodes [aut, cre] (<https://orcid.org/0000-0001-9921-1091>)

Initial release

QDC