Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986),
Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343
Quartet is an R package that calculates the Quartet distance between two trees: a measure of their similarity based on the number of shared four-taxon subtrees.
The package uses the
tqDist algorithm. Unlike many other implementations,
it distinguishes between quartets that are contradicted by one tree,
and quartets that are simply absent due to a lack of resolution (i.e. the presence
Quartet makes this distinction in both the quartet metric
QuartetStatus) and the partition metric (i.e. Robinson-Foulds distance;
Install and load the library from CRAN as follows:
If you're feeling brave, you can install the development version thus:
You will need Rtools installed in order to build the development version from source.
Brodal G.S., Fagerberg R., Pedersen C.N.S. 2004. Computing the quartet distance between evolutionary trees in time O(n log n). Algorithmica. 38:377–395.
Estabrook G.F., McMorris F.R., Meacham C.A. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Zool. 34:193–200.
Robinson D.F., Foulds L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131–147.
Sand A., Holt M.K., Johansen J., Brodal G.S., Mailund T., Pedersen C.N.S. 2014. tqDist: a library for computing the quartet and triplet distances between binary or general trees. Bioinformatics. 30:2079–2080. https://doi.org/10.1093/bioinformatics/btu157
Smith, M.R. (2019) Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets. Biology Letters. In production.
Steel, M. and Penny, D. Distributions of tree comparison metrics: some new results. Syst. Biol. (1993) 42 (2): 126-141. https://doi.org/10.1093/sysbio/42.2.126