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	×	Contig file	×
Exclusively absent genes	✓	×	×	×	×	×	×
Subset Analysis	✓	×	×	×	×	×	×
Atypical GC analysis	✓	×	×	×	×	×	×
Distribution of core, accessory and unique genome	✓	×	×	×	×	×	×
KEGG pathway distribution	✓	×	×	×	×	×	×
Pan-genome profile analysis	✓	✓	✓	✓	×	×	×
Size of core and pan-genome	✓	✓	×	×	×	✓	×
Extraction of core, accessory and unique genome sequence	✓	✓	×	×	×	×	✓
Evolutionary analysis	✓	✓	×	✓	×	✓	✓
Functional distribution analysis (COG)	✓	×	×	✓	✓	×	✓
Protein/gene clustering	✓	✓	×	✓	✓	✓	✓
Input data from user	✓	✓	✓	✓	×	✓	×
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	~3 m	>6 m	48 sec	29–200 m	NA	~10 m	>1 hr
Performance	Very Fast	Fast	Fast	Slow	Slow	Slow	Slow

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