reroot.md

Gotree: toolkit and api for phylogenetic tree manipulation

Commands

reroot

This command reroots a tree in two ways:

1. gotree reroot outgroup : Using an outgroup. If the outgroup is not monophyletic, 2 possibilities: 1) By default (--strict=false) it takes the lca of given tips to reroot the tree, and print a warning, 2) if --strict is given, it exits with an error.
2. gotree reroot midpoint: At midpoint.

Usage

General command

Usage:
  gotree reroot [command]

Available Commands:
  midpoint    Reroot trees at midpoint
  outgroup    Reroot trees using an outgroup

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

Examples

• Reroot a random tree using an outgroup in a file

outgroup.txt

Tip2
Tip4
Tip7

gotree generate yuletree --seed 10 -o outtree1.nw
gotree reroot outgroup -l outgroup.txt -i outtree1.nw -o outtree2.nw
gotree draw svg -w 200 -H 200  -i outtree1.nw -o commands/reroot_1.svg
gotree draw svg -w 200 -H 200  -i outtree2.nw --with-branch-support --support-cutoff 0.5 -o commands/reroot_2.svg

Initial random Tree	Rerooted Tree

• Reroot a random tree using an outgroup in commandline

gotree generate yuletree --seed 10 -o outtree1.nw
gotree reroot outgroup -i outtree1.nw -o outtree2.nw Tip2 Tip4 Tip7
gotree draw svg -w 200 -H 200  -i outtree1.nw -o commands/reroot_1.svg
gotree draw svg -w 200 -H 200  -i outtree2.nw --with-branch-support --support-cutoff 0.5 -o commands/reroot_2.svg

• Reroot a random tree using an outgroup in commandline, and remove the outgroup

gotree generate yuletree --seed 10 -o outtree1.nw
gotree reroot outgroup --remove-outgroup -i outtree1.nw -o outtree2.nw Tip2 Tip4 Tip7
gotree draw svg -w 200 -H 200  -i outtree1.nw -o commands/reroot_5.svg
gotree draw svg -w 200 -H 200  -i outtree2.nw --with-branch-support --support-cutoff 0.5 -o commands/reroot_6.svg

Initial random Tree	Rerooted Tree without the outgroup

• Reroot a random tree at midpoint

gotree generate yuletree --seed 10 -o outtree1.nw
gotree reroot midpoint -i outtree1.nw -o outtree2.nw 
gotree draw svg -w 200 -H 200  -i outtree1.nw -o commands/reroot_3.svg
gotree draw svg -w 200 -H 200  -i outtree2.nw --with-branch-support --support-cutoff 0.5 -o commands/reroot_4.svg

Initial random Tree	Rerooted Tree at Midpoint