Skip to content

Cmpnets Command

Jump to bottom
Berk Alp Yakici edited this page Mar 3, 2022 · 1 revision

Cmpnets

Computes the dissimilarity between two phylogenetic networks. Measures that are currently implemented are:

  • Tree-based measure: -m tree
  • Tripartition-based measure: -m tri
  • Cluster-based measure: -m cluster
  • Reduction-based measure (Nakhleh, L. (2010)): -m luay
  • Rooted Network Branch Score (rNBS) (Yakici, B. (2022)) measure: -m rnbs
  • Average Path Distance (APD) (Yakici, B. (2022)) measure: -m apd
  • Normalized Average Path Distance (NormAPD) (Yakici, B. (2022)) measure: -m normapd
  • Weighted Average Path Distance (WAPD) (Yakici, B. (2022)) measure: -m wapd
  • Normalized Weighted Average Path Distance (NormWAPD) (Yakici, B. (2022)) measure: -m normwapd

Usage

The networks must be specified in the Rich Newick Format.

cmpnets network_ident1 network_ident2 -m [tree|tri|cluster|luay|rnbs|apd|normapd|wapd|normwapd] [resultOutputFile]
Argument Description Mandatory
network_ident1 The name of the first network. mandatory
network_ident2 The name of the second network. mandatory
-m [tree|tri|cluster|luay|rnbs|apd|normapd|wapd|normwapd] Characterization mode. 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;

Output

If tree-based, tripartition-based, or cluster-based measures are used, then 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)
  • 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.

If rNBS, APD, or WAPD based measures are used, this program returns only one number:

  • The dissimilarity.

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.

Clone this wiki locally