Computational protocol: A phylogenetic examination of the primary anthocyanin production pathway of the Plantae

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Protocol publication

[…] Multiple alignments of DFR, ANS, F3′H, F3GT and F3′5′H DNA and amino acid orthologues were constructed using the CLUSTAL X v1.8 software (Thompson et al. ). All alignment settings were employed at default values.Phylogenetic trees were generated from the genetic distances provided by the CLUSTAL X analysis using the neighbor-joining method (Saitou and Nei ) and bootstrap analyses (Felsenstein ) consisting of 1,000 replicates were performed. The neighbor-joining trees were visualized with the TREEVIEW program (Page ). Bootstrap values less than 500 are not included on cladograms.We performed additional Maximum Likelihood (ML), Randomized Axelerated Maximum Likelihood (RaxML), Parsimony (MP), and Bayesian (Maximum Clade Credibility) analyses of the DNA and protein alignments using PhyML 3.0 (Guindon et al. ), Trex (Stamatakis ), MEGA 5.05 (Tamura et al. ), and BEAST (Drummond et al. ), respectively. These additional analyses were performed using default settings. […]

Pipeline specifications

Software tools Clustal W, TreeViewX, RAxML, PhyML, MEGA, BEAST
Application Phylogenetics
Chemicals Anthocyanins