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] |