Markov Clustering

Markov Clustering (MCL) is a graph clustering program (van Dongen & Abreu-Goodger, 2012) that can be used in combination a pairwise blastp output to infer phamilies of homologous proteins.

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 MCL:

   (pdm_utils)> conda install -c bioconda mcl -y
   

3. Test whether MCL has been successfully installed:

   (pdm_utils)> mcl --help
   

If successful, a detailed description of the software’s options should be displayed.

If unsuccessful, an error message should be displayed, such as:

-bash: mcl: command not found