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Computes the distance between two phylogenetic networks, based on their topologies. Three measures are currently implemented:
- Tree-based measure. (-m tree)
- Tripartition-based measure. (-m tri)
- Cluster-based measure. (-m cluster)
- Reduction-based measure (Nakhleh, L. (2010)). (-m luay)
The networks must be specified in the Rich Newick Format.
This program returns three numbers: the false negative rate (roughly, the trees/tripartitions/clusters found in the first network but not the second, divided by the number of trees/tripartitions/clusters in the first network), the false positive rate (roughly, the trees/tripartitions/clusters found in the second network but not the first, divided by the number of trees/tripartitions/clusters in the second network), and the average of the two rates (their sum divided by 2).
If reduction-based measure is used, this program returns only one number: the distance.
Usage
| Code Block | ||
|---|---|---|
| ||
cmpnets network_ident1 network_ident2 -m [tree|tri|cluster|luay] [resultOutputFile]
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network_ident1 | The name of the first network. | mandatory |
network_ident2 | The name of the second network. | mandatory |
-m [tree|tri|cluster|luay] | Characterization mode. One of | mandatory |
resultOutputFile | Optional file destination for command output. | optional |
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- L. Nakhleh and L.S. Wang. Phylogenetic networks: properties and relationship to trees and clusters. LNCS Transactions on Computational Systems Biology II, pages 82--99, 2005. LNBI #3680.
- Nakhleh, L. (2010). A metric on the space of reduced phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 7(2), 218-222.