Although there is an increasingly vaster literature on co-phylogenetic 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 algorithms do the host-parasite reconciliation analysis using an event-based model, where the events include in general (a subset of) co-speciation, 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. The main problem with this approach is that the cost of the events strongly influences the reconciliation obtained.
To deal with this problem, we developed an algorithm, called Coala (which stands for “COevolution Assessment by a Likelihood-free Approach”), for estimating the frequency of the events based on an approximate Bayesian computation approach. The paper presenting Coala may be found here.
The code of Coala is available here. Downloading Coala imposes full acceptance of the CeCILL license.
A documentation on how to use Coala may be found here. Finally, the nexus files used as input in the paper of Coala can be recovered here.
Contacts: Christian Baudet, Marie-France Sagot, and Blerina Sinaimeri
