Computational protocol: The Evolution of the Four Subunits of Voltage-Gated Calcium Channels: Ancient Roots, Increasing Complexity, and Multiple Losses

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Protocol publication

[…] Putative Cav homologs were detected in GenBank (nr), Broad Institute and Joint Genome Institute databases through BLAST. Transcript clusters were translated to proteins. Accession numbers of proteins used in all phylogenetic analyses can be found in supplementary table S1, Supplementary Material online. Protein models were aligned using MUSCLE and low-quality alignment regions were removed by TrimAl (; ). ProtTest was used to find the most suitable model for phylogeny reconstruction () and this model was used to reconstruct a maximum-likelihood tree with PhyML (). 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. […]

Pipeline specifications

Software tools MUSCLE, trimAl, ProtTest, PhyML, MrBayes
Applications Phylogenetics, Nucleotide sequence alignment
Diseases Migraine Disorders
Chemicals Calcium