unroot.md

Gotree: toolkit and api for phylogenetic tree manipulation

Commands

unroot

This command unroots a set of input trees. If a tree is already unrooted it does nothing. Otherwise it places the new pseudo root on a trifurcated node and removes the old root. When removing the old root, two branches have to be merged. Length of the new branch will be the sum of the two merged branches, and its support will be the maximum.

             ------C         
             |z	         
    ---------*	                       ------C 
    |x       |t	                 x+y   |z	   
ROOT*        ------B   =>    A---------*ROOT   
    |y		                       |t	   		 
    ---*A                              ------B 

Usage

General command

Usage:
  gotree unroot [flags]

Flags:
  -i, --input string    Input tree (default "stdin")
  -o, --output string   Collapsed tree output file (default "stdout")

Examples

• Generate a rooted random tree, and unroots it

gotree generate yuletree -r --seed 10 -o outtree1.nw
gotree unroot -i outtree1.nw -o outtree2.nw
gotree draw svg -w 200 -H 200 -i outtree1.nw -o commands/unroot_1.svg
gotree draw svg -w 200 -H 200 -i outtree2.nw -o commands/unroot_2.svg

Initial random Tree	Unrooted tree