Pangenomic profiles regarding the random benchmarks of the singleton-less data set with 10 genomes. Pangenomic profiles regarding the singleton-less dataset generated with default values of variation (0.3% indel rate, 0.3% loss rate and 0% duplication rate) from which 10 genomes were extracted randomly from the 100 individuals phylogenetic tree. For each possible number of genomes (1 to 10) that may be involved by a gene family, the table reports the amount of gene families involving the specific number of genomes. The real value refers to the actual number of families in the synthetic dataset
Genomes . | Real value . | GET_HOM. . | micropan . | PanDelos . | PanGeT . | PanOCT . | Panseq . | PanX . | PGAP . | Roary . |
---|---|---|---|---|---|---|---|---|---|---|
1 | 0 | 60 | 20 | 11 | 3 | 2 | 1496 | 19 | 206 | 6677 |
2 | 19 | 89 | 663 | 333 | 2 | 0 | 23 | 116 | 635 | 10 |
3 | 0 | 2 | 1 | 5 | 1 | 0 | 105 | 0 | 2 | 1 |
4 | 0 | 0 | 1 | 1 | 1 | 0 | 113 | 0 | 2 | 0 |
5 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | 4 | 0 |
6 | 0 | 1 | 0 | 2 | 3 | 1 | 22 | 0 | 3 | 0 |
7 | 2 | 8 | 14 | 316 | 43 | 6 | 340 | 4 | 29 | 0 |
8 | 11 | 79 | 648 | 327 | 615 | 660 | 0 | 110 | 622 | 0 |
9 | 13 | 30 | 0 | 13 | 0 | 0 | 0 | 9 | 0 | 0 |
10 | 645 | 546 | 6 | 11 | 0 | 0 | 0 | 507 | 0 | 0 |
Total fam. | 690 | 815 | 1355 | 1020 | 669 | 669 | 2099 | 766 | 1503 | 6688 |
Genomes . | Real value . | GET_HOM. . | micropan . | PanDelos . | PanGeT . | PanOCT . | Panseq . | PanX . | PGAP . | Roary . |
---|---|---|---|---|---|---|---|---|---|---|
1 | 0 | 60 | 20 | 11 | 3 | 2 | 1496 | 19 | 206 | 6677 |
2 | 19 | 89 | 663 | 333 | 2 | 0 | 23 | 116 | 635 | 10 |
3 | 0 | 2 | 1 | 5 | 1 | 0 | 105 | 0 | 2 | 1 |
4 | 0 | 0 | 1 | 1 | 1 | 0 | 113 | 0 | 2 | 0 |
5 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | 4 | 0 |
6 | 0 | 1 | 0 | 2 | 3 | 1 | 22 | 0 | 3 | 0 |
7 | 2 | 8 | 14 | 316 | 43 | 6 | 340 | 4 | 29 | 0 |
8 | 11 | 79 | 648 | 327 | 615 | 660 | 0 | 110 | 622 | 0 |
9 | 13 | 30 | 0 | 13 | 0 | 0 | 0 | 9 | 0 | 0 |
10 | 645 | 546 | 6 | 11 | 0 | 0 | 0 | 507 | 0 | 0 |
Total fam. | 690 | 815 | 1355 | 1020 | 669 | 669 | 2099 | 766 | 1503 | 6688 |
Pangenomic profiles regarding the random benchmarks of the singleton-less data set with 10 genomes. Pangenomic profiles regarding the singleton-less dataset generated with default values of variation (0.3% indel rate, 0.3% loss rate and 0% duplication rate) from which 10 genomes were extracted randomly from the 100 individuals phylogenetic tree. For each possible number of genomes (1 to 10) that may be involved by a gene family, the table reports the amount of gene families involving the specific number of genomes. The real value refers to the actual number of families in the synthetic dataset
Genomes . | Real value . | GET_HOM. . | micropan . | PanDelos . | PanGeT . | PanOCT . | Panseq . | PanX . | PGAP . | Roary . |
---|---|---|---|---|---|---|---|---|---|---|
1 | 0 | 60 | 20 | 11 | 3 | 2 | 1496 | 19 | 206 | 6677 |
2 | 19 | 89 | 663 | 333 | 2 | 0 | 23 | 116 | 635 | 10 |
3 | 0 | 2 | 1 | 5 | 1 | 0 | 105 | 0 | 2 | 1 |
4 | 0 | 0 | 1 | 1 | 1 | 0 | 113 | 0 | 2 | 0 |
5 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | 4 | 0 |
6 | 0 | 1 | 0 | 2 | 3 | 1 | 22 | 0 | 3 | 0 |
7 | 2 | 8 | 14 | 316 | 43 | 6 | 340 | 4 | 29 | 0 |
8 | 11 | 79 | 648 | 327 | 615 | 660 | 0 | 110 | 622 | 0 |
9 | 13 | 30 | 0 | 13 | 0 | 0 | 0 | 9 | 0 | 0 |
10 | 645 | 546 | 6 | 11 | 0 | 0 | 0 | 507 | 0 | 0 |
Total fam. | 690 | 815 | 1355 | 1020 | 669 | 669 | 2099 | 766 | 1503 | 6688 |
Genomes . | Real value . | GET_HOM. . | micropan . | PanDelos . | PanGeT . | PanOCT . | Panseq . | PanX . | PGAP . | Roary . |
---|---|---|---|---|---|---|---|---|---|---|
1 | 0 | 60 | 20 | 11 | 3 | 2 | 1496 | 19 | 206 | 6677 |
2 | 19 | 89 | 663 | 333 | 2 | 0 | 23 | 116 | 635 | 10 |
3 | 0 | 2 | 1 | 5 | 1 | 0 | 105 | 0 | 2 | 1 |
4 | 0 | 0 | 1 | 1 | 1 | 0 | 113 | 0 | 2 | 0 |
5 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | 4 | 0 |
6 | 0 | 1 | 0 | 2 | 3 | 1 | 22 | 0 | 3 | 0 |
7 | 2 | 8 | 14 | 316 | 43 | 6 | 340 | 4 | 29 | 0 |
8 | 11 | 79 | 648 | 327 | 615 | 660 | 0 | 110 | 622 | 0 |
9 | 13 | 30 | 0 | 13 | 0 | 0 | 0 | 9 | 0 | 0 |
10 | 645 | 546 | 6 | 11 | 0 | 0 | 0 | 507 | 0 | 0 |
Total fam. | 690 | 815 | 1355 | 1020 | 669 | 669 | 2099 | 766 | 1503 | 6688 |
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