Description

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

cmpnets network_ident1 network_ident2 -m [tree|tri|cluster|luay] [resultOutputFile]

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 tree, tri, cluster, or luay.

mandatory

resultOutputFile

Optional file destination for command output.

optional

Examples

#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;

Command References

  • L. Nakhleh, J. Sun, T. Warnow, R. Linder, B.M.E. Moret, and A. Tholse. Towards the development of computational tools for evaluating phylogenetic network reconstruction methods. In Proc. 8th Pacific Symp. on Biocomputing (PSB03), pages 315--326. World Scientific Pub., 2003.
  • B.M.E. Moret, L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme. Phylogenetic networks: modeling, reconstructibility, and accuracy. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1):13--23, 2004.
  • L. Nakhleh and L.S.Wang. Phylogenetic networks, trees, and clusters. In Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA 05), pages 919--926, 2005. LNCS #3515.
  • 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.

See Also

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