Table 1 Comparison of pan-genome analysis tools (MSA = multiple sequence alignment)
From: Reference-agnostic representation and visualization of pan-genomes
| Â | Gene based | Genome based | Reference agnostic | Alignment method | Largest genome tested | References |
|---|---|---|---|---|---|---|
PanX | \(\checkmark\) | Â | Â | Pairwise alignment using diamond | Microbial genomes | [6] |
PGAP | \(\checkmark\) | Â | \(\checkmark\) | All-pairs alignment and BLAST-all | Microbial genomes | [8] |
PGAP-X | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | MSA using progressiveMauve | Microbial genomes | [12] |
PPanGGOLiN | \(\checkmark\) | Â | Â | Uses gene families | 1000s of microbial genomes | [9] |
PanSeq | Â | \(\checkmark\) | Â | Pairwise alignment | Not mentioned | [11] |