Author: Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.
Title: A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species Document date: 2019_6_4
ID: telmxmp4_14
Snippet: Second, we removed exons if the species did not all agree on the exon structure. Specifically, we removed exons if all species did not agree on the aligned exon boundaries or if exon sequences differed too much in length. For phylogenetic analysis, where all genes are used in aggregate to fit a single tree, we required exact agreement in exon lengths. For gene-level positive selection analysis we required exons differ by no more than 1%. This cut.....
Document: Second, we removed exons if the species did not all agree on the exon structure. Specifically, we removed exons if all species did not agree on the aligned exon boundaries or if exon sequences differed too much in length. For phylogenetic analysis, where all genes are used in aggregate to fit a single tree, we required exact agreement in exon lengths. For gene-level positive selection analysis we required exons differ by no more than 1%. This cutoff was chosen because we observed it to be a transition point to high-gap exons in our data (SI Appendix, Fig. S1 ). Fig. 2 D-F are based on the latter threshold, and SI Appendix, Fig. S4 , shows the equivalent figures for the former.
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