Given a gene tree and a species tree (e.g., Fig. 1), Notung-2.6 will determine:
Notung-2.6 calculates the Duplication/Loss Score of a tree using the formula:
D/L Score = cL*losses + cD*duplications + cCD*conditionalDuplications
The values of cL, cD, and cCD may be set by the user.
These items can be seen in Notung's GUI (Fig. 1) or presented in a text file, generated from the command line.
|Fig. 1a: Gene Tree
Fig. 1c: Reconciled Gene Tree
Fig. 1b: Species Tree
This is an example of Notung-2.6 text file output. It shows the results of the gene tree shown in Fig. 1a reconciled with the species tree shown in Fig. 1b. This output is easily parsible, allowing it to fit into automated processes for high throughput genomic analysis.