A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.

We developed the MIXR software to detect and remove alternate consensus runs (available at http://github.com/hawkjo/mixr). The MIXR algorithm finds the maximum alternate-consensus-run score for each hypothesis bipartition of species and removes exons which overlap runs with significant scores-or species if removing exons would eliminate the entire alignment (see flowchart in SI Appendix, Fig. S3 ). To implement this algorithm outline, we needed to define three things: hypothesis bipartitions of species, the alternate-consensus-run scoring function, and the method used to determine significance.