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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 int 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
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cmpnets network_ident1 network_ident2 -m [tree|tri|cluster|luay] [result output fileresultOutputFile] |
network_ident1 | The name of the first network. | mandatory | |
network_ident2 | The name of the second network. | mandatory<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ab4319de-85b2-4bce-b23b-63e99a65e62f"><ac:plain-text-body><![CDATA[ | |
-m [tree|tri|cluster|luay] | Characterization mode. One of | mandatory | ]]></ac:plain-text-body></ac:structured-macro> |
result output file resultOutputFile | Optional file destination for command output. | optional |
Examples
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#NEXUS
BEGIN NETWORKS;
Network net1 = ((a,(b,(c)x#1)),((d,x#1),e));
Network net2 = ((((a, (c)x#1), d), (b, x)), e);
END;
BEGIN PHYLONET;
Cmpnets net1 net2 -m cluster;
END;
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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.