Computational protocol: The ubiquitin conjugating enzyme, TaU4 regulates wheat defence against the phytopathogen Zymoseptoria tritici

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Protocol publication

[…] The online alignment program webPRANK was used to generate an amino acid alignment, which was then edited using the software Jalview. The evolutionary history was inferred by using the Maximum Likelihood method based on the Jones et al. w/freq. model. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. The initial tree for the heuristic search was obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using a JTT model. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 5.5679)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 4.3710% sites). The analysis involved 16 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 101 positions in the final dataset. Evolutionary analyses were conducted in MEGA6. […]

Pipeline specifications

Software tools PRANK, Jalview, MEGA
Application Phylogenetics
Organisms Zymoseptoria tritici, Triticum aestivum, Human poliovirus 1 Mahoney