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.
TQDist(trees)TQAE(trees)
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).
List of phylogenetic trees, of class list or
multiPhylo.
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.
Brodal2013Quartet
Estabrook1985Quartet
Holt2014Quartet
Sand2014Quartet
CompareQuartets(), QuartetStatus()