Right now it seems that only nodes in the array tree can be flipped to modify the appearance of the tree. It would be convenient if nodes in the gene tree can be flipped as well.
Secondly, in the special case where the array tree and the gene tree are identical (i.e. not microarray data, but for instance a distance matrix for phylogeny, where every seq is compared to every seq [not what I am doing, but issue identical]) then it would be nice if a flip in an array tree node was 'linked' to the corresponding node in the gene tree [to keep the two trees identical, and to keep the diagonal symetry these arrays have].
The second part is probably harder to pull off and less needed than the first.
Love the program, it has made my life much easier so far!!