MMseqs2 is a suite of tools for rapid searching and clustering of protein and nucleotide sequences (:ref:`Steinegger and Söding, 2017 <bibliography>`). This software is required only if gene phamilies need to be identified using MMseqs2 in the phamerate pipeline. Complete, detailed installation instructions are provided by the developers on the project's :mmseqs2:`GitHub page <>`. The following instructions provide an example of how it can be installed on your local MacOS or Ubuntu machine.
Open a Terminal window and start the Conda environment:
> conda activate pdm_utils (pdm_utils)>
The most straightforward option is to use Conda to install MMseqs2:
(pdm_utils)> conda install -c bioconda -c conda-forge mmseqs2=13.45111 -y
Test whether MMseqs2 has been successfully installed:
(pdm_utils)> mmseqs cluster -h
If successful, a detailed description of the software's options should be displayed.
If unsuccessful, an error message should be displayed, such as:
-bash: mmseqs: command not found