Check out TreeMap 3.

TREEMAP 2.0ß

A Macintosh® program for the analysis of how dependent phylogenies are related, by cophylogeny mapping.

© Copyright, 2002 Michael A. Charleston* and Roderic D. M. Page†

Development of this program has been supported by NERC and the Royal Society

*School of Information Technologies, Sydney Bioinformatics and the Centre for Mathematical Biology; Sydney University, Camperdown, Sydney, NSW 2006, Australia.
†Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.

E-mail Michael Charleston at m•charleston AT usyd•edu•au or Rod Page at r•page AT bio•gla•ac•uk

Alert! TreeMap3 is coming. I am re-writing it in Java and it's coming along nicely. I am willing to let you have a development version, but it comes with NO guarantees.

TREEMAP is a Macintosh program that performs cophylogeny mapping from a dependent evolutionary tree (e.g., a group of parasites) into an independent one (e.g., the hosts of those parasites), in order to recover the best possible coevolutionary explanation for the relationship between the two (Page & Charleston, 1998). The archetypal example is of the coevolution of pocket gophers and their chewing lice (Page & Hafner, 1996).

A manual is still hasn't been written. Write to me and ask!

Version 2.02ß Download here

Bug fixes:

  • Was filtering out all guaranteeably non-optimal sub-solutions during jungle construction, even if the option had not been checked: this has been fixed.

Additional features:

  • New statistical test: the "Cherry Picking Test", to determine whether the significant part of congruence between H and P is due to associations between pairs of siblings at the tips of both trees (manuscript in prep.) "unbound" option on jungle bounds for each category (number of codivergences / duplications; number of losses; host switches; total number of non-codivergence events / total cost).
  • Log file "TreeMapLogFile.txt" automatically generated.
  • Summary descriptions of all resulting maps listed to the Log window.
  • Now takes into account timing information on host or associate tree. The relative times taken from branch lengths can be used to constrain jungle construction (and therefore make it faster!).
  • Jungle construction and significance testing dialogs are now tabbed.

Other stuff:

  • Numerous speed-ups, mostly from using new branch-and-bound method.

Version 2.0ß – New features, in no particular order:

  • Jungles are now implemented. This means
    • All solutions are found, by exhaustive search (previous heuristics had to be used).
    • All host switches can be dealt with consistently (including weakly incompatible switches).
    • There is no explicit optimality criterion: all solutions which could be optimal for some event cost scheme (cost of duplication, host switch and loss events) are presented; you can also opt to present all feasible maps (but the number of these grows exponentially!).
  • Much faster branch-and-bound search.
  • Option to produce all feasible solutions (memory notwithstanding) prior to filtering out guaranteeably non-optimal ones.
  • Plot of relative frequency in presented solutions of host switches in the host tree.
  • Significance testing, by randomizing the associate tree and measuring how often randomized associate trees fit as well as the given one. There are several new randomization test statistics available, and the standard error of the estimation on significance value is given.
  • Tabbed dialog boxes for your viewing pleasure.
  • Ability to save Macintosh graphics files (PICT format) for a selection of reconstructions.
  • Temporal information in the host and parasite trees can now be accommodated.
  • Lots of bug fixes.

You are welcome to use this software free of charge but the authors accept no responsibility for the veracity of the results and make no representation of the application's bug-free-ness, correctness, or suitability for your analysis. If you are in doubt we strongly recommend that you contact Michael Charleston or Rod Page.

We do assert that the logo is rather nice.

Download

Once you've downloaded it, just double-click and it should expand itself with the example files.
Please join the mailing list in order to be updated with new versions and bug fixes, and to let us know if you have suggestions for future versions.

 

Known Bugs and Problems

BUGS

This is a beta version. There may still be bugs!

If you really think you've found one, please let us know.

Some of the ones we do know about are listed below.

  • We don't know of any bugs at the moment. This will, no doubt, change.

PROBLEMS

Memory: TREEMAP finds all the globally optimal maps – it is an exact solution and requires a lot of memory! If it runs out, try either giving it more using the Get Info… in the Finder, or constrain the acceptable solutions more at the outset. Permitting very few non-codivergence events, particularly host switches, makes the solution much quicker, but at the expense of not necessarily knowing that the solutions you get are all of the potentially optimal ones. Bear in mind that the less restrictive you have to make these bounds to get a feasible solution, the less likely you are to get a significant match between the two trees.

THINGS WE’D LIKE IN TREEMAP

  • Ability to draw polytomies. We don't rate this as a high priority though since we do not believe there are good theoretical methods of dealing with them.
  • Better bounds during jungle construction – current ones are a big improvement but tighter ones are theoretically possible.
  • Inclusion of “failure to diverge” event, without too much increase in computational complexity.
  • Ability to handle reticulate phylogenies (such as caused by hybridization and recombination).
  • Plots showing relative frequencies of host switches on the host tree among reconstructions.
  • Some kind of "consensus" method for maps.
  • Inclusion of multiple sets of associations.
  • A better Switch Frequency Plot, perhaps just showing the numbers of times in the current set of solutions that a switch occurs (at present this is shown by a shade of grey).

References

Charleston, M. A. 1998. Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149:191-223. (pdf)

Page, R. D. M., & Hafner, M.S. 1996. Molecular phylogenies and host-parasite cospeciation: gophers and lice as a model system. Pages 255-270 in New uses for new phylogenies (Harvey, P.H., Leigh Brown, A.J., Maynard Smith, J., & Nee, S., eds.). Oxford University Press, Oxford.

Page, R. D. M. and Charleston, M. A. 1998. Trees within trees: phylogeny and historical associations. Trends in Ecology and Evolution 13(9):356-359. (pdf)

Last modified: Friday, January 6, 2006