The program Parsnp could be used to quickly infer a core-genome from a collection of closely related FASTA-formatted genome sequence files (one per considered isolate) contained inside a forder $indir with the following command line:
Of note, the overall running time could be improved by using multiple threads with option -p. This will generate a XMFA-formatted multiple sequence alignment of the core-genome named parsnp.xmfa inside the specified output directory $outdir. However, a FASTA-formatted file $outfile containing the concatenation of every aligned locally collinear block could be obtained with the associated program harvesttools: