Notung 2.8 does transfers! Notung 2.8 does phylogenomics!
Notung 2.8 is a reconciliation engine for the Duplication, Transfer, Loss, Incomplete Lineage Sorting (DTLI) model  that supports phylogenomic analysis. Notung's new phylogenomics option supports integrated analysis of large collections of gene families drawn from a set of genomes. In addition to reporting the events inferred for individual trees, this function aggregates and summarizes results across all reconciled gene trees and all nodes or branches of the species tree:
The integrated results from all reconciled gene families supports stratigraphic analysis of gene age relative to the species tree, co-evolution of gene families with related function, and investigation of genome-scale evolutionary trends, such as whole genome duplications, bursts of lateral transfer activity, and massive loss characteristic of genome reduction.
Notung was written by Benjamin Vernot, Aiton Goldman, Maureen Stolzer, Han Lai, Minli Xu, Deepa Sathaye, and Dannie Durand and is based on novel algorithms for DTLI-model reconciliation , tree rearrangement  and non-binary reconciliation [2,3]. 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
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary
This work was supported in part by NSF Grant DBI1262593. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.