Description

This script adds bootstrap support values from a bootstrap pseudoreplicate tree file (newick format) to a MrBayes tree (MrBayes nexus format) with posterior probabilities, and outputs the tree with combined support values in newick format.

Instructions

• Clone the repository.

git clone https://github.com/laelbarlow/combine_branch_supports.git

• Install the dependencies listed in the YAML file using conda (these include ETE3 and RAxML).

cd combine_branch_supports
mamba env create --file conda envs/boots_on_mb.yaml

• Ensure that your input trees have the same set of taxon names, and that the taxon names are simple alphanumeric strings (otherwise there may be errors in parsing).

• Use the script as follows:

python3 boots_on_mb.py <MrBayes consensus tree file NEXUS> <Bootstrap tree file NEWICK> <Output tree file NEWICK>

• Visualize output using FigTree.