Selected article for: "beta distribution and likelihood ratio test"
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_50
    Snippet: Positive Selection Analysis. Positive selection analysis was performed on the 10,650 orthologous genes alignments that had at least six species and 30 amino acids represented in the alignment. For each analysis, we used the species tree generated in this study. Using PAML (61), each alignment was fit to the M8 and M8a codon models, both performed with the f61 codon model. Both the M8 and M8a models assume the dN/dS value for a given aligned codon.....
    Document: Positive Selection Analysis. Positive selection analysis was performed on the 10,650 orthologous genes alignments that had at least six species and 30 amino acids represented in the alignment. For each analysis, we used the species tree generated in this study. Using PAML (61), each alignment was fit to the M8 and M8a codon models, both performed with the f61 codon model. Both the M8 and M8a models assume the dN/dS value for a given aligned codon is either a draw from a binned beta distribution (with fit parameters a and b) or a draw from a floating bin with parameter dN/dS = ω. The parameter ω can float to values >1 in M8 and is set to ω = 1 for M8a. P values were calculated via χ 2 test on twice the difference in reported log likelihoods of the two models, a likelihood-ratio test of nested models. GO category enrichment among positively selected genes was performed with the STRING database online software (101

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