Main tool : pangolin
Full documentation: https://cov-lineages.org/resources/pangolin.html
Phylogenetic Assignment of Named Global Outbreak LINeages
# run Pangolin in the default mode (usher). Can optionally supply --analysis-mode usher
pangolin /pangolin/pangolin/test/test_seqs.fasta -o /data/test_seqs-output-pusher
# run Pangolin in the fast/pangolearn mode. Can use either --analysis-mode fast or --analysis-mode pangolearn
pangolin /pangolin/pangolin/test/test_seqs.fasta --analysis-mode pangolearn -o /data/test_seqs-output-plearn