Table 1.
Summary overview of qualitative features of pan-genome tools implemented in this study
|
Method |
Software |
Input |
Graph output |
Pan-genome |
Sequence homology |
Paralogue identification |
|---|---|---|---|---|---|---|
|
Roary (v3.13.0) |
Conda package |
GFF3 |
DOT |
Directed graph |
blast |
Synteny |
|
Ptolemy (v1.0) |
Java executable |
FASTA+GFF |
GFA |
Directed graph |
minimap2 |
Graph-based |
|
PPanGGoLin (v1.0.13) |
Conda package |
GBK or FASTA |
GEXF |
Undirected graph |
MMseq2 |
Synteny |
|
PIRATE (v1.0.3) |
Conda package |
GFF3 |
GFA |
Directed graph |
blast (/DIAMOND) |
Synteny |
|
Panaroo (v1.1.2) |
Conda package |
GFF3 |
GML |
Directed graph |
CD-HIT |
Synteny |