MMseqs2

MMseqs2 is a suite of tools for rapid searching and clustering of protein and nucleotide sequences (Steinegger and Söding, 2017). 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 GitHub page. The following instructions provide an example of how it can be installed on your local MacOS or Ubuntu machine.

MacOS and Ubuntu installation

1. Open a Terminal window and start the Conda environment:

   > conda activate pdm_utils
   (pdm_utils)>
   

2. The most straightforward option is to use Conda to install MMseqs2:

   (pdm_utils)> conda install -c bioconda -c conda-forge mmseqs2=13.45111 -y
   

3. 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