Selected article for: "iq tree and maximum likelihood"
Author: Andrew Rambaut; Edward C Holmes; Verity Hill; Aine OToole; John McCrone; Chris Ruis; Louis du Plessis; Oliver Pybus
Title: A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology
  • Document date: 2020_4_19
    • ID: l7ymcyw7_22
    Snippet: We downloaded all SARS-CoV-2 genomes (at least 29,000bp in length) from GISAID on April 9th 2020. We trimmed the 5' and 3' untranslated regions and retained those genomes with at least 95% coverage of the reference genome (Wuhan-Hu-2019, GenBank accession MN908947). We aligned these sequences using MAFFT's FFT-NS-2 algorithm and default parameter settings (Katoh et al. 2002) . We then estimated a maximum likelihood tree using IQ-TREE 2 (Minh et a.....
    Document: We downloaded all SARS-CoV-2 genomes (at least 29,000bp in length) from GISAID on April 9th 2020. We trimmed the 5' and 3' untranslated regions and retained those genomes with at least 95% coverage of the reference genome (Wuhan-Hu-2019, GenBank accession MN908947). We aligned these sequences using MAFFT's FFT-NS-2 algorithm and default parameter settings (Katoh et al. 2002) . We then estimated a maximum likelihood tree using IQ-TREE 2 (Minh et al. 2020 ) using the GTR+G model of nucleotide substitution (Tavaré 1986; Yang 1994) , default heuristic search options, and ultrafast bootstrapping with 1000 replicates (Minh, Nguyen, and von Haeseler 2013) .

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