TQDist() and TQAE() are convenience functions that writes a list of
trees to text files that can be processed by the C implementation of tqDist
Sand2014Quartet.
tqDist is then called, and the temporary file is deleted when analysis is
complete.
Arguments
- trees
List of phylogenetic trees, of class
listormultiPhylo.
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).
Details
Quartets can be resolved in one of five ways, which Brodal2013;textualQuartet and Holt2014;textualQuartet distinguish using the letters A-E, and Estabrook1985;textualQuartet refer 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.