This is an implementation of Lima-Mendez et al. (DOI: 10.1093/molbev/msn023) method of clustering of bacteriophages based on gene shared content.
- Prodigal - ORFs caller (DOI: 10.1186/1471-2105-11-119)
- Diamond - homology search engine (DOI: https://doi.org/10.1038/nmeth.3176)
- MCL - clustering algorithm (DOI: https://doi.org/10.1137/040608635)
If everithing in PATH and executable:
LMCLUST phages_genomes.fasta
Otherwise, add paths inside the LMCLUST script