Computational protocol: Analysis of Soluble Protein Contents from the Nematocysts of a Model Sea Anemone Sheds Light on Venom Evolution

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[…] The boundaries of CAP and Astacin domains were determined according to PFAM. The domains were aligned using MUSCLE and for the SCP domains low quality alignment regions were removed by TrimAl (Capella-Gutierrez et al. ; Edgar ). ProtTest was used to find the most suitable model for phylogeny reconstruction (Abascal et al. ). For both domain alignments, the maximum-likelihood (ML) phylogenetic tree was constructed using PhyML with the WAG Model (+I + G), which got the highest score in the ProtTest analysis. Support values were calculated using 100 bootstrap replicates. A Bayesian tree was constructed using MrBayes version 3.1.2 with the same model. The run lasted 5,000,000 generations and every 100th generation was sampled. We estimated that the Bayesian analysis reached convergence when the potential scale reduction factor reached 1.0. […]

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