This is a draft document describing the new software TREEMAP3, which has been a very long time coming. I have been spurred on to re-write the thing in Java, partly because I like programming in new languages (to me) but mostly because I was greatly embarrassed to learn that some of my most respected colleagues have been holding on to old Macintosh computers that run Classic, just so they can run TREEMAP2.
I've just received a very kind request for TM3 and I thought I may as well just upload the development version for people to have a look at, and this may work as further incentive (coupled with their polite urgings!) to finish it. Thus, this is NOT a final version; it does NOT do all the things you want it to do, but it will, and it will do more. And at this point I am very happy to entertain suggestions on what other features and things could go in.
So far, TM3 has the following functionality, which was already in TM2:
It does not (but will!)
TM3 is written completely differently from TM1 and TM2. For a start it's in a different language, Java, while TM1 and TM2 were in C++. I like both these languages, but have opted for Java for its promise of portability, and the comparative ease of GUI development.
TM3 also uses the concept of the liana, which I introduced in my "Principles of cophylogenetic maps" book chapter, available from http://www.springerlink.com/content/61023248h5873375/.
TM3 will use lianas to handle reticulate phylogenies, and my aim is to get it to handle multi-host parasites this way too.
It now outputs a jungle constructed using the constraints given to the tanglegram (using the admittedly horrible interface as yet), in the "dot" format. You can visualise the graphs using dot or GraphVis http://www.graphviz.org/doc/info/lang.html.
These will be good.