Installation

Installation of PhyloFisher via conda

1. Install conda and mamba:
   curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -o Mambaforge-Linux-x86_64.sh
bash Mambaforge-Linux-x86_64.sh
2. Prepare a conda virtual environment:
   mamba create -n fisher
3. Activate the conda environment:
   conda activate fisher
4. Add the Bioconda & Conda-Forge Anaconda Cloud channels to your channels:
   conda config --append channels bioconda
conda config --append channels conda-forge
   
5. Install PhyloFisher:
   mamba install phylofisher

Notes:

• After you finish using PhyloFisher, use conda deactivate to deactivate the fisher conda virtual environment.
  

Installation of forest_local.py & ParaSorter locally (including Windows)

Installation of forest_local.py (a standalone version of forest.py) and ParaSorter on a users local machine is required for downstream steps in the PhyloFisher workflow. Although the entire PhyloFisher software package does not run on Windows, this minimal download will. This download will provide users (including Windows users) the graphical tree parsing aspects of the package on their local machines. This minimal download of forest_local.py and ParaSorter can be retrieved from the ”ParaSorter” section of PhyloFisher GitHub Repository.

Further documentation on the usage of both forest_local.py and Parasorter can be found in steps 9 and 10 in the ”Detailed Example Workflow” section of this manual respectively.