Despite a rapidly growing literature on cophylogenetic reconstructions for studying host-parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Many of the most used algorithms do the host-parasite reconciliation analysis using an event-based model, where the events include in general (a subset of) cospeciation, duplication, loss, and host-switch. All known event-based methods then assign a cost to each type of event in order to find a reconstruction of minimum cost. One of the problems with this approach is that there may be a huge number of optimal solutions or at least solutions that are close to optimal. Thus, it is of interest to be able to systematically compare and visualize whole collections of reconciliations between a specified pair of trees.

To investigate this problem, we consider various metrics on the set of all possible reconciliations between a pair of trees, including some new metrics and some that have been defined before.

For more details about our methodology, please refer to our paper:

• K. Huber, V. Moulton, M.-F. Sagot, B. Sinaimeri, Exploring and visualizing spaces of tree reconciliations, submitted.

Download

• The input of the program is a text file containing all the reconciliations to study, obtained as a result of the Task 3 using Eucalypt.
• The program to calculate the distances between any two reconciliations from a set of reconciliations can be downloaded here
• The scripts to perform the statistical analysis can be downloaded here.