WQDC {MSCquartets}

Compute Weighted Quartet Distance Consensus tree from gene tree data

Description

Compute the Weighted Quartet Distance Consensus (Yourdkhani and Rhodes 2020) estimate of a species tree from gene tree data. This is a consistent estimator of the unrooted species tree topology and all internal branch lengths.

Usage

WQDC(
  genetreedata,
  taxanames = NULL,
  method = fastme.bal,
  omit = FALSE,
  terminal = 1
)

Arguments

genetreedata

gene tree data that may be supplied in any of 3 forms:

1. a character string giving the name of a file containing gene trees in Newick

2. a multiPhylo object containing gene trees

3. a resolved quartet table, 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 leaves out unresolved quartets, FALSE treats them as 1/3 of each resolution; ignored if genetreedata is given as a resolved quartet table

terminal

non-negative branch length to supply for terminal branches whose length cannot be inferred by WQDC

Details

This function is a wrapper which performs the steps of reading in a collection of gene trees, tallying quartets, estimating quartet internal branch lengths, computing the weighted quartet distance between taxa, building a tree, and adjusting edge lengths, to give a consistent estimate of the metric species tree in coalescent units under the MSC.

If the gene tree data indicates some quartets experienced little to no incomplete lineage sorting, this algorithm tends to be less topologically accurate than QDC (which infers no metric information) or WQDCrecursive (which gives better topologies, and reasonably accurate lengths for short edges, though long edge lengths may still be unreliable).

Value

an unrooted metric tree of type phylo

References

Yourdkhani S, Rhodes JA (2020). “Inferring metric trees from weighted quartets via an intertaxon distance.” Bul. Math. Biol., 82(97). doi:10.1007/s11538-020-00773-4.

See Also

quartetTable, quartetTableResolved, quartetTableDominant, quartetWeightedDist, WQDCrecursive, WQDS, QDC

Examples

gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=taxonNames(gtrees)
stree=WQDC(gtrees,tnames[1:6])
write.tree(stree)
plot(stree)