consensus_tree.py – This script outputs a majority consensus tree given a collection of input trees.

Description:

Usage: consensus_tree.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_dir

Input folder containing trees

-o, --output_fname

The output consensus tree filepath

[OPTIONAL]

-s, --strict

Use only nodes occurring >50% of the time [default: False]

Output:

The output is a newick formatted tree compatible with most standard tree viewing programs

basic usage: given a directory of trees ‘jackknifed_trees’, compute the majority consensus and save as a newick formatted text file:

consensus_tree.py -i jackknifed_trees -o consensus_tree.tre