--maxrejects 10000 --minqt 0.7. We use marker gene specific thresholds that were calibrated in Milanese et al. Nature Comm. 2019 to distinguish between different species. For example,
COG0049is a conserved gene with threshold
COG0124is evolutionary under less pressure having a threshold of
No genes, no marker genes have been detected in the fasta file;
No match, marker genes have been detected in the input genome, but there is no match to the specI taxonomy;
Inconsistent, marker genes have been detected and map to the specI database, but half of the genes map to one specI and the other half to another specI;
Consistent, the majority of the genes agree on one specI.
Consistentmatches, we did a 10-fold cross-validation.