Selected article for: "bat virus and pangolin virus"
Author: Aiping Wu; Peihua Niu; Lulan Wang; Hangyu Zhou; Xiang Zhao; Wenling Wang; Jingfeng Wang; Chengyang Ji; Xiao Ding; Xianyue Wang; Roujian Lu; Sarah Gold; Saba Aliyari; Shilei Zhang; Ellee Vikram; Angela Zou; Emily Lenh; Janet Chen; Fei Ye; Na Han; Yousong Peng; Haitao Guo; Guizhen Wu; Taijiao Jiang; Wenjie Tan; Genhong Cheng
Title: Mutations, Recombination and Insertion in the Evolution of 2019-nCoV
  • Document date: 2020_3_2
    • ID: jmrg4oeb_42
    Snippet: The SNPs of each sequence were defined as the sites variant from the reference sequence. The ancestral sequence of the phylogenetic tree was used as the reference sequence, which was estimated by python package TimeTree using Jukes-Cantor model and default settings. Site with the unsolved nucleotide N and gap was ignored. The site 10 number of the SNP was decided by sequentially combined the CDS sequences in the whole genome. The phylogenetic tre.....
    Document: The SNPs of each sequence were defined as the sites variant from the reference sequence. The ancestral sequence of the phylogenetic tree was used as the reference sequence, which was estimated by python package TimeTree using Jukes-Cantor model and default settings. Site with the unsolved nucleotide N and gap was ignored. The site 10 number of the SNP was decided by sequentially combined the CDS sequences in the whole genome. The phylogenetic tree and the matching SNP for the tips was plotted by ggtree. The geo-distribution and genotype of strains with SNP sites in Wuhan and other areas were plotted by ggplot2. The SNP sites of 2019-nCoV were compared with SARSlike virus in one bat and eight pangolin genome sequences. The pangolin sequences 15 EPI_ISL_410543 and EPI_ISL_410544 were removed for too many unsolved nucleotides. The adjacent nucleotide of the two SNP sites 8517 and 27641 were extracted from the alignment. The translation-reading frame was inferred by using the GenBank annotations for the EPI_ISL_402125 strain.

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