calculate neighborhoods for internal nodes

[ajo2995]

Since the gene tree is often displayed with many collapsed branches it would be nice to summarize the neighborhood conservation for genes in the clade.

We can walk the gene tree and assign a neighborhood to an internal node based on the (two) child nodes.

By definition, the central gene should remain in that position in the parent neighborhood. Similarly, any other pair of genes from the same gene tree in the same relative position could be assigned to the parent. The non-trivial part is dealing with local differences (genes only in one child, tandem duplications, inversions, etc.)

Lets not make it too complicated in case we are able to bring in real synteny information at a later time

[ajo2995]

this is an ancestral reconstruction problem