Gene Tree Reconciliation

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.

By default, cL = 1, cD = 1.5, and cCD = 0.

These items can be seen in Notung's GUI (Fig. 1) or presented in a text file, generated from the command line.

Fig. 1: Gene Tree Reconciliation

Fig. 1a: Gene Tree

Fig. 1c: Reconciled Gene Tree

Fig. 1b: Species Tree

Fig 2:Command Line Output

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.

COST: 2.5

Duplication         L. Bound            U. Bound
=================== =================== ====================
n4                  tetrapod            N/A

Duplications: 1

Species             No. of Losses
=================== ===================
tetrapod            0
HUMAN               0
FROG                1
MOUSE               0
mammalia            0

Losses: 1