Table 1 OGC generation strategies and tools used in this study
From: Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses
Clustering | Paralog splitting | Identity threshold | Software | Ref |
|---|---|---|---|---|
De novo | Orthology-based | None (e-val < 0.001) | panX | [33] |
De novo | Orthology-based | None (e-val < 0.001) | OrthoFinder | [32] |
De novo | Synteny-based | 80%, 95% | Roary | [34] |
De novo | None | 50%, 80% | MMseqs2, PanACoTA | |
De novo | None | 50%, 80% | CD-HIT | [28] |
Reference db | n.a | None (e-val < 0.001) | eggNOG-mapper | [44] |