HHSD

hhsd can be used to perform Hierarchical Heuristic Species Delimitation from multilocus genetic data.

Installation instructions

Prerequisites

• Users must have python 3.9+ installed. Check your current version with python --version.
• Users must create and activate a dedicated virtual environment for the installation of the package. See: https://docs.python.org/3/tutorial/venv.html for detailed instuctions on how this can be accomplished.
• Create a dedicated folder (in the directory where you normally install your programs), and move your terminal to that folder.
• Activate your dedicated virtual environment for hhsd before beginning installation.

- Linux

Installation on linux can be accomplshed via the following set of commands:

git clone https://github.com/abacus-gene/hhsd

cd hhsd

pip install .

- macOS

Installation on macOS is also relatively straightforward. Make sure that you are using the pip version specific to python3.

git clone https://github.com/abacus-gene/hhsd

cd hhsd

pip3 install .

- Windows

Windows installations are slightly more complicated.

• If git is aldready installed, run the command: git clone https://github.com/abacus-gene/hhsd
• If not, download the code by visiting https://github.com/abacus-gene/hhsd/archive/refs/heads/main.zip. Rename the zip file to hhsd.zip, and then uncompress.

Then, install the program as expected:

cd hhsd

pip install .

Checking your install

To check if hhsd was installed successfully, open your command line of choice, and type:

hhsd

This should result in a greeting message similar to the following:

hhsd version 1.1.0
BPP executable at '<path to bpp>' is present and functional.
12 cores available
specify control file for analysis with --cfile

---

Detailed instructions

Details on the operation of the program, including best practices, and a thorough explanation of parameter syntax can be found in the manual.