Selected article for: "cc ND international license and model fit"
Author: Joana Damas; Graham M. Hughes; Kathleen C. Keough; Corrie A. Painter; Nicole S. Persky; Marco Corbo; Michael Hiller; Klaus-Peter Koepfli; Andreas R. Pfenning; Huabin Zhao; Diane P. Genereux; Ross Swofford; Katherine S. Pollard; Oliver A. Ryder; Martin T. Nweeia; Kerstin Lindblad-Toh; Emma C. Teeling; Elinor K. Karlsson; Harris A. Lewin
Title: Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates
  • Document date: 2020_4_18
    • ID: 6ne76rh1_53
    Snippet: Site-models M7 (null model) and M8 (alternative model) were used to identify ACE2 sites undergoing positive selection in mammals. Both M7 and M8 estimate ⍵ using a beta distribution and 10 rate categories per site with ⍵<=1 (neutral or purifying selection), but with an additional 11 th category allowing ⍵ >1 (positive selection) in M8. A likelihood ratio test (LRT) calculated as 2*(lnL alt -lnL null ), comparing the fit of both null and alt.....
    Document: Site-models M7 (null model) and M8 (alternative model) were used to identify ACE2 sites undergoing positive selection in mammals. Both M7 and M8 estimate ⍵ using a beta distribution and 10 rate categories per site with ⍵<=1 (neutral or purifying selection), but with an additional 11 th category allowing ⍵ >1 (positive selection) in M8. A likelihood ratio test (LRT) calculated as 2*(lnL alt -lnL null ), comparing the fit of both null and alternative model likelihoods was carried out, with a p-value 17 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.16.045302 doi: bioRxiv preprint calculated assuming a chi-squared distribution. Sites showing evidence of positive selection were identified by a significant (>0.95) Bayes Empirical Bayes (BEB) score, and validated by visual inspection of the protein alignment. To explore order-specific instances of positive selection, separate multiple sequence alignments and gene trees for Chiroptera (N=37), Cetartiodactyla (N=45), Carnivora (N=44), Rodentia (N=46) and Primates (N=39) were also generated and explored using M7 vs. M8 in CODEML.

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