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In the terminal, navigate to the directory containing the unzipped phylosift   Run  ./phylosift search contig\_file\_name  For example:  ./phylosift search /Users/microBEnet/Desktop/Data-Genomes/Pantoea\_Tatumella/tatumella/tatumella.final.scaffolds.fasta.contigs.fsa   Note: The first time you run PhyloSift it has to download a marker gene database so it may take a few minutes.