Tarzan Download

Start Tarzan with java -cp tarzan-v0.9.jar jungle/Tarzan

Preferred java version is jdk1.3.

An example of a tree pair that be can used with Tarzan can be downloaded here.

Explanation of the example: The cophylogeny of African brood parasite finches (Vidua sp.) and their finch hosts (family Estrildae) has been studied by Sorenson et al. [2]. The parasite finches are host specialists that mimic the songs and the nestling mouth markings of their hosts. The phylogeny of the Vidua species was compared in [2] with the phylogeny of the estrildid finch hosts and compared with divergence time estimates for both groups.

In [1] we have analyzed the data from [2] data with Tarzan by including the information about divergence times into the analysis. In order to translate the timing information into labels we defined 5 time zones (0-1.5 Myr, >1.5 – 3.0 Myr, >3.0 – 4.5 Myr, >4.5 – 6.0 Myr, >6.0 Myr). All nodes of the estrildid host tree and the Vidua parasite tree as given in Figure 4 in [2] have been assigned labels. The trees that that were used by Tarzan are the given example trees. Some changes that have been made to ensure that the tree nodes have outdegree at most 2 and details of the assignment of the time zones are described in [1].

[1] D. Merkle, M. Middendorf
Reconstruction of the Cophylogenetic History of Related Phylogenetic Trees with Divergence Timing Information
Theory of Biosciences, 4: 277-299, 2005.

[2] M.D. Sorenson, C.N. Balakrishnan, R.B. Payne
Clade-limited colonization in brood parasitic finches (Vidua spp.)
Systematic Biology, 53: 140-153, 2004.