Pairwise Distances from a Phylogenetic Network

cophenetic.networx computes the pairwise distances between the pairs of tips from a phylogenetic network using its branch lengths.

Usage

# S3 method for class 'networx'
cophenetic(x)

Arguments

x

an object of class networx.

Value

an object of class dist, names are set according to the tip labels (as given by the element tip.label of the argument x).

See also

cophenetic for the generic function, neighborNet to construct a network from a distance matrix

Author

Klaus Schliep

Examples

example(neighborNet)
#> 
#> nghbrN> data(yeast)
#> 
#> nghbrN> dm <- dist.ml(yeast)
#> 
#> nghbrN> nnet <- neighborNet(dm)
#> 
#> nghbrN> plot(nnet)

#> 
#> nghbrN> plot(nnet, type="outline")

cophenetic(nnet)
#>            Sbay       Skud       Smik       Spar       Scer       Scas
#> Skud 0.15679569                                                       
#> Smik 0.17138720 0.15382927                                            
#> Spar 0.16838347 0.15082553 0.12360062                                 
#> Scer 0.17717456 0.16108716 0.13763679 0.08678458                      
#> Scas 0.34958331 0.35210510 0.34479766 0.34179392 0.34350386           
#> Calb 0.54518366 0.54770545 0.54039800 0.53739427 0.53910421 0.52768392
#> Sklu 0.38096004 0.38397653 0.38238343 0.37937970 0.38167995 0.39014046
#>            Calb
#> Skud           
#> Smik           
#> Spar           
#> Scer           
#> Scas           
#> Calb           
#> Sklu 0.54213286