Also check out Notung 2.7 Beta : reconciliation with gene duplication, gene loss, horizontal gene transfer, incomplete lineage sorting.
Notung 2.6 is a software tool that offers a unified framework for incorporating duplication/loss parsimony into phylogenetic tasks, including
All of Notung 2.6's functions (except resolution) are applicable to binary trees. In addition, Notung 2.6 can reconcile or root a non-binary gene tree with a binary species tree or a binary gene tree with a non-binary species tree. Notung 2.6 can also rearrange a non-binary gene tree with a binary species tree. Rearrangement of binary gene trees with non-binary species trees, and reconciliation, rooting, and rearrangement of of non-binary gene trees with non-binary species trees are currently open, algorithmic problems.
These operations can be carried out via a graphical user interface that facilitates exploratory data analysis. Notung 2.6 also offers a command-line interface enabling the user to analyze a large number of gene trees automatically.
Notung 2.6 was written by Benjamin Vernot, Aiton Goldman, Maureen Stolzer and Dannie Durand and is based on a novel algorithms for tree rearrangement  and non-binary reconciliation [1,2]. Notung is an extension of a program first presented by Chen, Durand and Farach-Colton . The graphical user interface was constructed using the tree visualization library provided by FORESTER (version 1.92). . For more information, contact mailto:firstname.lastname@example.org
Hybrid Micro-Macroevolutionary Approach to Gene Tree