Selected article for: "multiple sequence and phylogenetic analysis"
Author: Xianding Deng; Wei Gu; Scot Federman; Louis Du Plessis; Oliver Pybus; Nuno Faria; Candace Wang; Guixia Yu; Chao-Yang Pan; Hugo Guevara; Alicia Sotomayor-Gonzalez; Kelsey Zorn; Allan Gopez; Venice Servellita; Elaine Hsu; Steve Miller; Trevor Bedford; Alexander Greninger; Pavitra Roychoudhury; Michael Famulare; Helen Y Chu; Jay Shendure; Lea Starita; Catie Anderson; Karthik Gangavarapu; Mark Zeller; Emily Spencer; Kristian Andersen; Duncan MacCannell; Suxiang Tong; Gregory Armstrong; Clinton Paden; Yan Li; Ying Zhang; Scott Morrow; Matthew Willis; Bela Matyas; Sundari Mase; Olivia Kasirye; Maggie Park; Curtis Chan; Alexander Yu; Shua Chai; Elsa Villarino; Brandon Bonin; Debra Wadford; Charles Y Chiu
Title: A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage
  • Document date: 2020_3_30
    • ID: cbc98t7x_33
    Snippet: is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.03. 27.20044925 doi: medRxiv preprint Phylogenetic analysis and genomic comparison Sequences were aligned using MAFFT v7.427 (24) under default settings and multiple sequence alignments were manually corrected. Phylogenetic trees were constructed in PhyML v3.3 (25) under an HKY+Γ 4 substitution model (26, 27) . The location of SNPs and gaps.....
    Document: is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.03. 27.20044925 doi: medRxiv preprint Phylogenetic analysis and genomic comparison Sequences were aligned using MAFFT v7.427 (24) under default settings and multiple sequence alignments were manually corrected. Phylogenetic trees were constructed in PhyML v3.3 (25) under an HKY+Γ 4 substitution model (26, 27) . The location of SNPs and gaps were extracted from alignments using a custom Python script and visualized using a custom R-script.

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