Installation

This page tells you how to install HybSuite step by step.

1. Install HybSuite via conda

(1) Prerequisites

  • Conda installation is required. If you don’t already have conda installed, see here for instructions on installing Anaconda or Miniconda.

(2) Step-by-step installation

To avoid dependency conflicts, creating a new conda environment for HybSuite is more recommended:

conda create -n hybsuite

And then, you can activate your newly-created conda environment and install hybsuite using the command below directly (from the specified channel):

conda activate hybsuite
conda install yuxuanliu::hybsuite

Before installing hybsuite, you can edit your ~/.condarc file as this to avoid installation issues about conda channels:

channels:
  - conda-forge
  - bioconda
  - yuxuanliu
  - defaults

(3) Verification

After installation, you can check the help menu of HybSuite to confirm successful installation by running:

hybsuite -h

2. Install HybSuite manually

(1) Prerequisites

  • Conda installation is required. If you don’t already have conda installed, see here for instructions on installing Anaconda or Miniconda.

(2) Package installtion

Directly clone the github repository:

git clone https://github.com/Yuxuanliu-HZAU/HybSuite.git

(3) Verification

After installation, you can check the help menu of HybSuite to confirm successful installation by running:

bash <absolute or relative path to HybSuite.sh> -h

(4) Dependencies installtion

The most convenient way to install all dependencies for HybSuite is directly running our script: HybSuite-master/Install_all_dependencies.sh to install all desired dependencies.
Before running this script, activate your target conda environment.

conda activate <conda_environment_name>
bash HybSuite-master/Install_all_dependencies.sh

Method 2: Install dependencies manually

If you fail to install some dependencies when running Install_all_dependencies.sh, then it is more advisable to install dependencies manually. Just follow the following steps:

conda create -n <conda_environment_name>
conda activate <conda_environment_name>
conda install conda-forge::mamba -y
mamba install python=3.9.15 -y
mamba install bioconda::hybpiper -y
mamba install bioconda::paragone -y
mamba install bioconda::amas -y
mamba install bioconda::sra-tools -y
mamba install conda-forge::pigz -y
conda install conda-forge::plotly -y
mamba install bioconda::newick_utils -y
mamba install bioconda::mafft -y
mamba install bioconda::trimal -y
mamba install bioconda::iqtree -y
mamba install bioconda::raxml -y
mamba install bioconda::raxml-ng -y
mamba install bioconda::aster -y
mamba install r
pip install ete3
pip install PyQt5
pip install phylopypruner
pip install phykit

R
install.packages("phytools")
install.packages("ape")

3. Dependencies


Last modified March 5, 2026: Update plotly.html (84cc3e0)