Summary of the main computational methodologies used by the reviewed tools in order to retrieve pangenomic content. PanGP is not included in the list since it does not provide an internal homology detection procedure
| Tool . | Alignment based . | Alignment free . | Bidirectional best hist . | Paralog specific . | Prior knowledge . | Protein domains . | Clustering . | Parameter free . |
|---|---|---|---|---|---|---|---|---|
| EDGAR | x | x | x | |||||
| Panseq | x | |||||||
| PGAT | x | |||||||
| PGAP | x | x | x | x | ||||
| PanOCT | x | x | x | x | ||||
| PanFunPro | x | x | x | x | ||||
| GET_HOMOLOGUES | x | x | x | |||||
| ITEP | x | x | x | |||||
| LS-BSR | x | x | ||||||
| Roary | x | x | x | x | ||||
| micropan | x | x | x | |||||
| BPGA | x | x | ||||||
| PanX | x | x | ||||||
| PanGeT | x | x | ||||||
| PanDelos | x | x | x | x | x |
| Tool . | Alignment based . | Alignment free . | Bidirectional best hist . | Paralog specific . | Prior knowledge . | Protein domains . | Clustering . | Parameter free . |
|---|---|---|---|---|---|---|---|---|
| EDGAR | x | x | x | |||||
| Panseq | x | |||||||
| PGAT | x | |||||||
| PGAP | x | x | x | x | ||||
| PanOCT | x | x | x | x | ||||
| PanFunPro | x | x | x | x | ||||
| GET_HOMOLOGUES | x | x | x | |||||
| ITEP | x | x | x | |||||
| LS-BSR | x | x | ||||||
| Roary | x | x | x | x | ||||
| micropan | x | x | x | |||||
| BPGA | x | x | ||||||
| PanX | x | x | ||||||
| PanGeT | x | x | ||||||
| PanDelos | x | x | x | x | x |
Summary of the main computational methodologies used by the reviewed tools in order to retrieve pangenomic content. PanGP is not included in the list since it does not provide an internal homology detection procedure
| Tool . | Alignment based . | Alignment free . | Bidirectional best hist . | Paralog specific . | Prior knowledge . | Protein domains . | Clustering . | Parameter free . |
|---|---|---|---|---|---|---|---|---|
| EDGAR | x | x | x | |||||
| Panseq | x | |||||||
| PGAT | x | |||||||
| PGAP | x | x | x | x | ||||
| PanOCT | x | x | x | x | ||||
| PanFunPro | x | x | x | x | ||||
| GET_HOMOLOGUES | x | x | x | |||||
| ITEP | x | x | x | |||||
| LS-BSR | x | x | ||||||
| Roary | x | x | x | x | ||||
| micropan | x | x | x | |||||
| BPGA | x | x | ||||||
| PanX | x | x | ||||||
| PanGeT | x | x | ||||||
| PanDelos | x | x | x | x | x |
| Tool . | Alignment based . | Alignment free . | Bidirectional best hist . | Paralog specific . | Prior knowledge . | Protein domains . | Clustering . | Parameter free . |
|---|---|---|---|---|---|---|---|---|
| EDGAR | x | x | x | |||||
| Panseq | x | |||||||
| PGAT | x | |||||||
| PGAP | x | x | x | x | ||||
| PanOCT | x | x | x | x | ||||
| PanFunPro | x | x | x | x | ||||
| GET_HOMOLOGUES | x | x | x | |||||
| ITEP | x | x | x | |||||
| LS-BSR | x | x | ||||||
| Roary | x | x | x | x | ||||
| micropan | x | x | x | |||||
| BPGA | x | x | ||||||
| PanX | x | x | ||||||
| PanGeT | x | x | ||||||
| PanDelos | x | x | x | x | x |
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