Phylogenetic trees in Newick format

This data set contains various exemples of phylogenetic trees in Newick format.

Usage

data(newick.eg)

Format

newick.eg is a list containing 14 character strings in Newick format.

Source

Trees 1 to 7 were obtained from the phylip software.

Trees 8 and 9 were obtained by Clémentine Carpentier-Gimaret.

Tree 10 was obtained from Treezilla Data Sets .

Trees 11 and 12 are taken from Bauwens and Díaz-Uriarte (1997).

Tree 13 is taken from Cheverud and Dow (1985).

Tree 13 is taken from Martins and Hansen (1997).

References

Bauwens, D. and Díaz-Uriarte, R. (1997) Covariation of life-history traits in lacertid lizards: a comparative study. American Naturalist, 149, 91--111.

Cheverud, J. and Dow, M.M. (1985) An autocorrelation analysis of genetic variation due to lineal fission in social groups of rhesus macaques. American Journal of Physical Anthropology, 67, 113--122.

Martins, E. P. and Hansen, T.F. (1997) Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist, 149, 646--667.

Examples

data(newick.eg)
newick2phylog(newick.eg[[11]])
#> Phylogenetic tree with 18 leaves and 17 nodes
#> $class: phylog
#> $call: newick2phylog(x.tre = newick.eg[[11]])
#> $tre: ((Sa,Sh)I1,((((Tl,(Mc,My)...Ls,Lv)I13)I14)I15)I16)Root; 
#> 
#>         class   length content                                     
#> $leaves numeric 18     length of the first preceeding adjacent edge
#> $nodes  numeric 17     length of the first preceeding adjacent edge
#> $parts  list    17     subsets of descendant nodes                 
#> $paths  list    35     path from root to node or leave             
#> $droot  numeric 35     distance to root                            
#> 
#>          class      dim   content                                   
#> $Wmat    matrix     18-18 W matrix : root to the closest ancestor   
#> $Wdist   dist       153   Nodal distances                           
#> $Wvalues numeric    17    Eigen values of QWQ/sum(Q)                
#> $Wscores data.frame 18-17 Eigen vectors of QWQ '1/n' normed         
#> $Amat    matrix     18-18 Topological proximity matrix A            
#> $Avalues numeric    17    Eigen values of QAQ matrix                
#> $Adim    integer    1     number of positive eigen values of QAQ    
#> $Ascores data.frame 18-17 Eigen vectors of QAQ '1/n' normed         
#> $Aparam  data.frame 17-3  Topological indices for nodes             
#> $Bindica data.frame 18-17 class indicator from nodes                
#> $Bscores data.frame 18-17 Topological orthonormal basis '1/n' normed
#> $Blabels character  17    Nodes labelling from orthonormal basis    
radial.phylog(newick2phylog(newick.eg[[7]]), circ = 1,
 clabel.l = 0.75)