Likelihood ratio tests (PAML) in <i>Anopheles</i> immunity genes between models that allow positive selection (M3, M2a, M8) and those that do not (M0, M1a, M7) and identification of sites exhibiting dN/dS ratio >1.
Aristeidis Parmakelis
Marina Moustaka
Nikolaos Poulakakis
Christos Louis
Michel A. Slotman
Jonathon C. Marshall
Parfait H. Awono-Ambene
Christophe Antonio-Nkondjio
Frederic Simard
Adalgisa Caccone
Jeffrey R. Powell
10.1371/journal.pone.0008885.t003
https://plos.figshare.com/articles/dataset/_Likelihood_ratio_tests_PAML_in_Anopheles_immunity_genes_between_models_that_allow_positive_selection_M3_M2a_M8_and_those_that_do_not_M0_M1a_M7_and_identification_of_sites_exhibiting_dN_dS_ratio_1_/536975
*<p>Significant <i>p-value</i> at 0.05 significance level; <i>df</i>: degrees of freedom.</p>a<p>This quantity is compared to the critical values of a chi-square distribution with the respective degrees of freedom.</p>b<p>Probability>0.95 in the Naive Empirical Bayes (NEB) analyses of PAML. Even though positive selection based on indications of the NEB analysis is questionable, we are reporting the results for within-gene comparative purposes.</p>c<p>Probability>0.99 in the Bayes Empirical Bayes (BEB) analyses of PAML.</p>d<p>Sites refer to amino acid positions of the proteins.</p>e<p>Letters in parentheses refer to the amino acid present at the site.</p><p>Sites in bold characters indicate those that were identified by HyPhy as well.</p>
2010-01-26 01:56:15
immunity
genes
models
sites
exhibiting