Table 2 Comparison of BPGA with other tools currently available for pan-genome analysis.
Features | BPGA | Roary27 | PanGP26 | PGAP28 | PGAT45 | Panseq25 | ITEP29 |
|---|---|---|---|---|---|---|---|
Input file/s | .GBK/.FAA/Matrix | .gff | Cluster/ Matrix | .FAA, .FFN & .PTT | Ć | Contig file | Ć |
Exclusively absent genes | ā | Ć | Ć | Ć | Ć | Ć | Ć |
Subset Analysis | ā | Ć | Ć | Ć | Ć | Ć | Ć |
Atypical GC analysis | ā | Ć | Ć | Ć | Ć | Ć | Ć |
Distribution of core, accessory and unique genome | ā | Ć | Ć | Ć | Ć | Ć | Ć |
KEGG pathway distribution | ā | Ć | Ć | Ć | Ć | Ć | Ć |
Pan-genome profile analysis | ā | ā | ā | ā | Ć | Ć | Ć |
Size of core and pan-genome | ā | ā | Ć | Ć | Ć | ā | Ć |
Extraction of core, accessory and unique genome sequence | ā | ā | Ć | Ć | Ć | Ć | ā |
Evolutionary analysis | ā | ā | Ć | ā | Ć | ā | ā |
Functional distribution analysis (COG) | ā | Ć | Ć | ā | ā | Ć | ā |
Protein/gene clustering | ā | ā | Ć | ā | ā | ā | ā |
Input data from user | ā | ā | ā | ā | Ć | ā | Ć |
Operating System | Windows, Linux and any Perl supported OS. | Linux | Windows & Linux | Linux | NA | Windows & Linux | Linux |
Mode of program | Standalone | Standalone | Standalone | Standalone | Online Database | Online & Standalone | Standalone |
Test dataset | S. pyogenes | S. typhi | E. coli | S. pyogenes | NA | S. pyogenes | Enterobacteria |
No. of genomes in test dataset | 28 | 24 | 30 | 11 | NA | 11 | 24 |
Time cost | ~3ām | >6ām | 48āsec | 29ā200ām | NA | ~10ām | >1āhr |
Performance | Very Fast | Fast | Fast | Slow | Slow | Slow | Slow |
