Computational protocol: Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza

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Protocol publication

[…] To perform phylogeny reconstruction, the protein sequence alignment was performed by using the MAFFT program []. The phylogenetic tree based on the alignment was reconstructed using the maximum likelihood method in MEGA5 [] with 1,000 replicates of bootstrap analysis. [...] Protein structure modeling was performed with the SWISS-MODEL service ( [] using the previously determined structure of 5-epi-aristolochene synthase M4 mutant ([], PDB id, 3lz9) as the modeling template. Models were visualized and analyzed using the program PyMOL. […]

Pipeline specifications

Software tools MAFFT, MEGA, PyMOL
Applications Phylogenetics, Protein structure analysis
Organisms Oryza sativa, Zea mays, Sorghum bicolor
Chemicals Carbon, Terpenes