Which alignment file can be used to create SNP matrix for clonal studies

[Firdoos071]

Hi everyone!

Snippy generates two different sized alignment files core.aln and core.full.aln. which alignment file will be used to create SNP matrix to study clonal samples? Whether Core.full.aln contains core plus accessory genomes as it is multiple times greater in size than core.aln

Thank You Firdoos