TQDist: Wrapper for tqDist

In ms609/SlowQuartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

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 ([e-mail])

References

• \insertRef

  Brodal2013Quartet

• \insertRef

  Estabrook1985Quartet

• \insertRef

  Holt2014Quartet

• \insertRef

  Sand2014Quartet

See Also

CompareQuartets(), QuartetStatus()

ms609/SlowQuartet documentation built on April 17, 2024, 11:23 a.m.