Notung is a software tool that offers a unified framework for incorporating duplication/loss parsimony into phylogenetic tasks, including
1. reconciling a gene tree with a species tree and estimating upper and lower bounds on the time of duplication;
2. rooting an unrooted gene tree by minimizing duplication and loss events;
3. rearranging a rooted gene tree in areas of weak sequence support to minimize the number of duplications and losses.
4. resolving a non-binary gene tree by fitting it to a binary species tree.
IAll of Notung functions (except resolution) are applicable to binary trees. In addition, Notung 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 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 also offers a command-line interface enabling the user to analyze a large number of gene trees automatically.
The license of this software is Freeware, you can free download and free use this calculator software.