R: Wrapper for tqDist

TQDist {Quartet}

R Documentation

Wrapper for tqDist

Description

Convenience function that takes a list of trees, writes them to the text file expected by the C implementation of tqDist (Sand et al. 2014). tqDist is then called, and the temporary file is deleted when analysis is complete.

Usage

TQDist(trees)

TQAE(trees)

Arguments

trees

List of phylogenetic trees, of class list or multiPhylo.

Details

Quartets can be resolved in one of five ways, which Brodal et al. (2013) and Holt et al. (2014) distinguish using the letters A–E, and Estabrook et al. (1985) refers to as:

A: s = resolved the same in both trees;
B: d = resolved differently in both trees;
C: r1 = resolved only in tree 1;
D: r2 = resolved only in tree 2 (the comparison tree);
E: u = unresolved in both trees.

Value

TQDist() returns the quartet distance between each pair of trees.

TQAE() returns the number of resolved quartets in agreement between each pair of trees ("A" in Brodal et al. 2013) and the number of quartets that are unresolved in both trees ("E" in Brodal et al. 2013).

Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

References

Brodal GS, Fagerberg R, Mailund T, Pedersen CNS, Sand A (2013). “Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree.” SODA '13 Proceedings of the Twenty-Fourth Annual ACM-SIAM Symposium on Discrete Algorithms, 1814–1832. doi:10.1137/1.9781611973105.130.
Estabrook GF, McMorris FR, Meacham CA (1985). “Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units.” Systematic Zoology, 34(2), 193–200. doi:10.2307/2413326.
Holt MK, Johansen J, Brodal GS (2014). “On the scalability of computing triplet and quartet distances.” In Proceedings of 16th Workshop on Algorithm Engineering and Experiments (ALENEX) Portland, Oregon, USA.
Sand A, Holt MK, Johansen J, Brodal GS, Mailund T, Pedersen CNS (2014). “tqDist: a library for computing the quartet and triplet distances between binary or general trees.” Bioinformatics, 30(14), 2079–2080. ISSN 1460-2059, doi:10.1093/bioinformatics/btu157.