Table 2.
Comparative benchmark analysis of the filtering performance of the GET_PHYLOMARKERS pipeline when run using the FastTree (FT) and IQ-TREE (IQT) maximum-likelihood algorithms, under default and high search-intensity levels.
| Test | FTdef | FThigh | IQTdef | IQThigh |
|---|---|---|---|---|
| Alignments passing the Phi recombination test | 127/239 (53.14%) | 125/239 (52.30%) | 125/239 (52.30%) | 127/239 (53.14%) |
| Outlier phylogenies (kdetrees test; k = 1.0) out of the indicated number of non-recombinant alignments | 22/127 (17.32%) passing: 105 | 18 (14.17%) passing: 107 | 19 (14.96%) passing: 106 | 22 (17.32%) passing: 105 |
| Alignments passing the phylogenetic signal (mean SH-alrt bipartition support; m ≥ 0.7) test | 98/105 (93.33%) | 99/107 (92.52%) | 52/106 (49.05%) | 55/105 (52.38%) |
| Concatenated top-scoring markers, lnL score, substitution model and number of independent searches | 98 markers | 99 markers | 52 markers | 55 markers |
| var. sites = 36,082 | var. sites = 35,509 | var. sites = 25,383 | var. sites = 26,988 | |
| lnL = −917444.522 | lnL = −899898.614 | lnL = −666437.563 | lnL = −707933.476 | |
| GTR+G | GTR+G | GTR+F+ASC+R6 | GTR+F+ASC+R6 | |
| Searches = 1 | Searches = 1 | Searches = 1 | Searches = 5 | |
| Total wall-clock time of runs on 50 cores | 0 h:13 m:39 s | 0 h:38 m:30 s | 1 h:22 m:18 s | 2 h:40 m:13 s |
The analyses were started with the stringently defined set of 239 consensus core-genome clusters computed by GET_HOMOLOGUES for a dataset of 119 genomes (112 Stenotrophomonas spp. and 7 Xanthomonas spp.).