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.

Note that in all three of our cleaning steps, we have tried to avoid filtering on sequence divergence as much as possible. This is because our intention is to perform positive selection analysis on the cleaned alignments, an analysis which measures the ratio between nonsynonymous and synonymous mutations. Filtering strategies based on whether the protein sequences agree will directly bias the data in favor of synonymous mutations, and the exon-length-matching and MIXR steps are expected to have this effect to some degree. However, to whatever degree this is true in our data, it will have a conservative effect, biasing the data to fewer rather than more significant hits in a positive selection analysis.