Computational protocol: Prevalence, Characterization, and Mycotoxin Production Ability of Fusarium Species on Korean Adlay (Coix lacrymal-jobi L.) Seeds

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Protocol publication

[…] The obtained sequences and other sequences retrieved from the previous study or in GenBank were initially aligned with the CLUSTAL X (v 2.0, 2007, the Conway Institute UCD Dublin, Dublin, Ireland) program [], were edited in BioEdit (v 7.0.1, Tom Hall, 2013, Ibis Biosciences, CA, USA), and were completed with manual adjustment. For the combined analysis, the genes were concatenated in a single nucleotide alignment. Maximum likelihood analysis was conducted using RAxML (v 7.2.8 HPC, The Exelixis Lab 2013, Scientific Computing Group, Heidelberg, Germany) by employing the GTRGAMMA model of nucleotide substitution. The robustness of the phylogram in the maximum likelihood analyses was evaluated by 1000 bootstrap replications. The best tree obtained from this search was edited in Mega (v 5.05, 2011, The Biodesign Institute, AZ, USA) []. […]

Pipeline specifications

Software tools Clustal W, BioEdit, RAxML, MEGA-V
Applications Phylogenetics, GWAS
Organisms Fusarium graminearum
Chemicals Zearalenone