- Major changes to the pairwise comparisons algorithm. Scoary now calculates the maximum number of contrasting pairs, and given that maximum number tests the maximum number of pairs that SUPPORT A -> B (AB-ab pairs) and the maximum number of pairs that OPPOSE A -> B (Ab-aB pairs). The opposite is true for genes where the odds ratio is < 1 (i.e. that indicate A -> b).
- The p-values reported from the pairwise comparisons is now a range. It reports the best (lowest) p-value, which comes from the maximum number of supporting pairs and the minimum number of opposing (given a set total), as well as the worst (highest) p-value, which comes from the minimum number of supporting pairs and the maximum number of non-supporting, given a set total number of pairings. It does this at each node in the tree.
- Scoary can now print the UPGMA tree that is calculated internally from the Hamming distances of the gene_presence_absence matrix. Do this by using the -u flag.
- The elapsed time will now print when finished.