--aaiflag) at a given threshold (by default 95%) that can be modified with the flag
--threshold. Finally, the representative genomes can be selected to reflect the highest genome quality (default) or to be the most "central" genome in the clade in ANI or AAI space (passing the
essential_genes, as well as a table (
genomospecies.tsv) with three columns: (1) a clade name, (2) the name of the representative genome, and (3) the names of all the members in the clade separated by commas. Additionally you can expect the subdirectory
representativesincluding assemblies (FastA files, nucleotides) of all representative genomes. This is the dereplicated set of genomes.