Jeepers it's been a while since I was on this.

It's official: the reticulate cophylogeny problem is NP-complete. Phew, I was worried about that. Thanks for this go to Ran Libeskind-Hadas, who did most of the work.

I've been thinking about multi-host parasites. These are a pain.
How to deal with them? The same PhD student (Rob) tells me that host specificity is really mucky and varies hugely among systems. It's so awful we don't know how best to represent it and solve it. I was hoping that we could just have "composite locations" on the host phylogeny but without restricting exactly which host lineages they can and can't include, there's the potential to explode the problem space even more, by approximately O(4^n), for n taxa on the host tree, which is yucky.

I've also been rewriting TreeMap in Java. It does stuff already, but I've not got it doing actual maps yet, only jungles.. TM3 will be awesome. It already has useful things like "untangle": when you have lots of edge crossings in your tanglegram and you can't untangle them, press the button and hey presto :-) It's just a heuristic, but it's cool.