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Table 1 Comparison of pan-genome analysis tools (MSA = multiple sequence alignment)

From: Reference-agnostic representation and visualization of pan-genomes

  Gene based Genome based Reference agnostic Alignment method Largest genome tested References
PanX \(\checkmark\)    Pairwise alignment using diamond Microbial genomes [6]
PGAP \(\checkmark\)   \(\checkmark\) All-pairs alignment and BLAST-all Microbial genomes [8]
PGAP-X \(\checkmark\) \(\checkmark\) \(\checkmark\) MSA using progressiveMauve Microbial genomes [12]
PPanGGOLiN \(\checkmark\)    Uses gene families 1000s of microbial genomes [9]
PanSeq   \(\checkmark\)   Pairwise alignment Not mentioned [11]