Selected article for: "likelihood method and model parameter"
Author: Xiaojun Li; Elena E. Giorgi; Manukumar Honnayakanahalli Marichann; Brian Foley; Chuan Xiao; Xiang-peng Kong; Yue Chen; Bette Korber; Feng Gao
Title: Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection
  • Document date: 2020_3_22
    • ID: 7v5aln90_23
    Snippet: The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.20.000885 doi: bioRxiv preprint Recombination Analyses SimPlot 3.5.15 (14) was used determine the percent identity of the query sequence to reference sequences. Potential recombinant regions among analyzed sequences were identified by sliding a 400bp-window at a 50bp-step across the alignment using the Kimura 2-parameter model. Phylogenet.....
    Document: The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.20.000885 doi: bioRxiv preprint Recombination Analyses SimPlot 3.5.15 (14) was used determine the percent identity of the query sequence to reference sequences. Potential recombinant regions among analyzed sequences were identified by sliding a 400bp-window at a 50bp-step across the alignment using the Kimura 2-parameter model. Phylogenetic trees were constructed by the maximum likelihood method using the GTR model (40) , and their reliability was estimated from 1,000 bootstrap replicates. The positions of analyzed sequence regions were based on those in the reference SARS-CoV-2 Wuhan-Hu-1 (MN908947). Recombination regions and breakpoints were also analyzed using the LANL database (41) tool RIP (16) .

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