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_48
Snippet: Finally, to determine significance, we build and score negative control sequences. The negative control sequences are constructed by shuffling all columns from all alignments which contain all species to construct sequences at least 100× as long as the longest alignment. For each alignment, we select the negative control sequences corresponding to the species in the alignment, truncate them to 100× the length of the alignment in question, and f.....
Document: Finally, to determine significance, we build and score negative control sequences. The negative control sequences are constructed by shuffling all columns from all alignments which contain all species to construct sequences at least 100× as long as the longest alignment. For each alignment, we select the negative control sequences corresponding to the species in the alignment, truncate them to 100× the length of the alignment in question, and find the maximum score for each hypothesis bipartition. Alternateconsensus-run scores larger than their corresponding negative control score thus have P values K 0.01, and are considered significant, to be removed as shown in flowchart SI Appendix, Fig. S3 . No multiple hypothesis correction is performed, conservatively removing borderline cases.
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