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Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
Snippy is a software tool for rapid haploid variant calling and core genome alignment.
ABRicate is a software tool for mass screening of contigs for antimicrobial resistance or virulence genes.
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
You can use these softwares as the following illustration graph.