Table 2.

Comparison of PanGFR-HM with other microbial pan-genome analysis resources.

Functional feature	PanGFR-HM†	EDGAR 2.0	Micro Scope	MetaRef
No. of genomes included	1293 (S.)	2160 (N.S.)	3871 (N.S.)	2818 (N.S.)
Pan-genome distribution	✓	✓	✓	✓
Pan, core profile (development) plots	✓	✓	✓	×
Strain wise pan-genome distribution	✓	✓	✓	×
Core-genome based phylogeny	✓	✓	×	×
Forming groups of strains	✓	✓	×	×
Sequence identity cut-off setting option	✓#	×	✓∗	×
Editable and interactive plots	✓	×	×	×
Pan-genome based phylogeny	✓	×	×	×
Strain wise sequence retrieval from pan-genome	✓	×	×	×
Exclusive gene distribution	✓	×	×	×
Exclusive COG and KEGG distribution	✓	×	×	×
Over/under-representation of functional classes	✓	×	×	×
Exclusive absence of genes	✓	×	×	×
COG and KEGG distribution of pan-genome	✓	×	×	×

^†Present tool, ^#40–90% (40, 50, 60, 70, 80, and 90%) identity cut-off options available, ^∗Only 50 and 80% identity cut-off option available, S., Specific to human microbiome, N.S., Non Specific, ✓-present, ×-absent. Features listed in italics are exclusive to PanGFR-HM.