read.tree.string {phybase}R Documentation

Read tree strings from a tree file

Description

This function reads tree strings in the parenthetical format from a tree file. The output of the function is a vector of tree strings that can be converted to a matrix of nodes by the function read.tree.nodes.

Usage

read.tree.string(file = "", format="nexus")

Arguments

file the tree file that contains trees in the parenthetical format.
format phylip or nexus

Details

The function can read NEXUS and PHYLIP tree files. It works for other types of tree files as long as the trees in the tree files are parenthetical trees. This function combining with write.tree.string can change the tree file format.

Value

tree a vector of tree strings.
names species names.
root TRUE for rooted trees, FALSE for unrooted trees

Author(s)

Liang Liu lliu@oeb.harvard.edu

See Also

write.tree.string, read.tree.nodes

Examples

##read rooted trees in PHYLIP format
cat("(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);",file = "phylip.tre", sep = "\n")
tree.string<-read.tree.string("phylip.tre")
tree.string

##read unrooted trees in NEXUS format
cat("#NEXUS
[ID: 4045516090]
begin trees;
   translate
       1 WW_7A03_1,
       2 WW_7H06_2,
       3 WW_7H05_1,
       4 WW_N03__5,
       5 WW_Snnr_1,
       6 WW_7P10__1,
       7 WW_7A05_1,
       8 WW_B03__1,
       9 WW_B04_1,
      10 WW_D07_9,
      11 WW_7K01_1,
      12 WW_7K04_1,
      13 WW_7N13_1,
      14 WW_M02_1,
      15 WW_N04_1,
      16 WW_UK6_1,
      17 WW_7A04_1,
      18 Pfuscatus_PF2_4,
      19 Pfuscatus_PF1_1,
      20 Pfuscatus_PF3_2,
      21 PCabietinus_331_1,
      22 PCabietinus_333_6,
      23 PCabietinus_336_1,
      24 PCcollybita_GB_1,
      25 PCtristis_GB_1,
      26 PCbrehmii_GB_1,
      27 Psibilatrix_GB_1,
      28 Pbonelli_GB_1,
      29 PTviridanus_1;
   tree rep.1 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000);
   tree rep.100 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000);
   tree rep.200 = (((((((((((((((16:0.100000,2:0.100000):0.100000,20:0.100000):0.100000,21:0.100000):0.100000,8:0.100000):0.100000,((19:0.100000,9:0.100000):0.100000,13:0.100000):0.100000):0.100000,23:0.100000):0.100000,27:0.100000):0.100000,5:0.100000):0.100000,26:0.100000):0.100000,((22:0.100000,28:0.100000):0.100000,11:0.100000):0.100000):0.100000,(24:0.100000,10:0.100000):0.100000):0.100000,6:0.100000):0.100000,(18:0.100000,((15:0.100000,14:0.100000):0.100000,(25:0.100000,12:0.100000):0.100000):0.100000):0.100000):0.100000,17:0.100000):0.100000,(7:0.100000,(3:0.100000,(1:0.100000,4:0.100000):0.100000):0.100000):0.100000,29:0.100000);
end;",file="tree.nexus")
tree.string<-read.tree.string("tree.nexus")
tree.string

[Package phybase version 1.1 Index]