Mowgli is a program for gene/species trees reconciliation analysis developed in C++. It is based on the model and algorithm of Doyon et al.  and the parsimony criterion: it seeks a Most Parsimonious Reconciliation (MPR for short) that explains the evolution of the gene family in terms of Duplications, Transfers, Losses, and Speciations (respectively denoted D, T, L, and S).Mowgli also takes into consideration uncertainty in the gene tree.
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J-P. Doyon, C. Scornavacca, K. Y. Gorbunov, G. Szollosi, V. Ranwez, and V. Berry.
An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers.
Lecture Notes in Computer Science, 2011, Volume 6398/2011, 93-108, DOI: 10.1007/978-3-642-16181-0_9