Selected article for: "best fit and likelihood tree"
Author: Takhampunya, Ratree; Korkusol, Achareeya; Pongpichit, Chalermpol; Yodin, Komsan; Rungrojn, Artharee; Chanarat, Nitima; Promsathaporn, Sommai; Monkanna, Taweesak; Thaloengsok, Sasikanya; Tippayachai, Bousaraporn; Kumfao, Naruemon; Richards, Allen L.; Davidson, Silas A.
Title: Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand
  • Document date: 2019_2_26
    • ID: 0gi6qzw0_33
    Snippet: PCR amplicons were purified using the QIAquick R PCR Purification Kit (Qiagen) according to the manufacturer's instructions. The PCR products were cycle-sequenced using an ABI BigDye TM Terminator v3.1 Cycle Sequencing Kit, ethanol precipitated, and run on a SeqStudio Genetic Analyzer (Applied Biosystems Thermo Fisher, Thailand). Sequences of each sample and pathogen were assembled using Sequencher TM ver. 5.1 (Gene Codes Corp., Ann Arbor, MI, Un.....
    Document: PCR amplicons were purified using the QIAquick R PCR Purification Kit (Qiagen) according to the manufacturer's instructions. The PCR products were cycle-sequenced using an ABI BigDye TM Terminator v3.1 Cycle Sequencing Kit, ethanol precipitated, and run on a SeqStudio Genetic Analyzer (Applied Biosystems Thermo Fisher, Thailand). Sequences of each sample and pathogen were assembled using Sequencher TM ver. 5.1 (Gene Codes Corp., Ann Arbor, MI, United States). The pathogen sequences were aligned with reference sequences retrieved from the GenBank database using the MUSCLE codon alignment algorithm (Edgar, 2004) . A maximum likelihood phylogenetic tree was then constructed from bacterial target gene(s) (Supplementary Table S1) using the best fit model of nucleotide substitution with bootstrapping (1000 replicates) in MEGA 6 (Tamura et al., 2013) .

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