Read New Hampshire eXtended format for trees
read_nhx(fn, txt)Full path to the tree file.
If no file is specified, trees can also be passed as a character scalar (see examples).
A list with the following elements:
tree An object of class ape
edge Edge annotations (length and other annotations)
nhx A list of annotations NHX
"NHX - New Hampshire eXtended [version 2.0]", https://en.wikipedia.org/wiki/Newick_format#New_Hampshire_X_format
Other reading:
panther-tree,
read_pli()
# Example directly extracted from
# https://sites.google.com/site/cmzmasek/home/software/forester/nhx
read_nhx(
txt = "(((ADH2:0.1[&&NHX:S=human], ADH1:0.11[&&NHX:S=human]):0.05[&&NHX:S=primates:D=Y:B=100],
ADHY:0.1[&&NHX:S=nematode],ADHX:0.12[&&NHX:S=insect]):0.1[&&NHX:S=metazoa:D=N],
(ADH4:0.09[&&NHX:S=yeast],ADH3:0.13[&&NHX:S=yeast], ADH2:0.12[&&NHX:S=yeast],
ADH1:0.11[&&NHX:S=yeast]):0.1 [&&NHX:S=Fungi])[&&NHX:D=N];"
)
#> $tree
#>
#> Phylogenetic tree with 8 tips and 4 internal nodes.
#>
#> Tip labels:
#> ADH2, ADH1,
#> ADHY, ADHX, ADH4, ADH3, ...
#> Node labels:
#> , unnamed0002, unnamed0001, unnamed0003
#>
#> Rooted; includes branch lengths.
#>
#> $edge
#> [,1] [,2]
#> [1,] "ADH2" ":0.1"
#> [2,] "ADH1" ":0.11"
#> [3,] "unnamed0001" ":0.05"
#> [4,] "ADHY" ":0.1"
#> [5,] "ADHX" ":0.12"
#> [6,] "unnamed0002" ":0.1"
#> [7,] "ADH4" ":0.09"
#> [8,] "ADH3" ":0.13"
#> [9,] "ADH2" ":0.12"
#> [10,] "ADH1" ":0.11"
#> [11,] "unnamed0003" ":0.1"
#>
#> $nhx
#> $nhx[[1]]
#> S
#> "human"
#>
#> $nhx[[2]]
#> S
#> "human"
#>
#> $nhx[[3]]
#> S D B
#> "primates" "Y" "100"
#>
#> $nhx[[4]]
#> S
#> "nematode"
#>
#> $nhx[[5]]
#> S
#> "insect"
#>
#> $nhx[[6]]
#> S D
#> "metazoa" "N"
#>
#> $nhx[[7]]
#> S
#> "yeast"
#>
#> $nhx[[8]]
#> S
#> "yeast"
#>
#> $nhx[[9]]
#> S
#> "yeast"
#>
#> $nhx[[10]]
#> S
#> "yeast"
#>
#> $nhx[[11]]
#> S
#> "Fungi"
#>
#>