Gene Tree Reconciliation

Given a gene tree and a species tree (e.g., Fig. 1), Notung-2.6 will determine:

• The duplications, conditional duplications, and losses that occurred
• Upper and lower bounds on the time of duplication and conditional duplication
• The cost (D/L Score) of the tree

  D/L Score = cL*losses + cD*duplications + cCD*conditionalDuplications

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