Computational protocol: A novel gene’s role in an ancient mechanism: secreted Frizzled-related protein 1 is a critical component in the anterior–posterior Wnt signaling network that governs the establishment of the anterior neuroectoderm in sea urchin embryos

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Protocol publication

[…] For the phylogenetic analysis, we used truncated amino acid sequences of the Fzl-CRD domains from each protein (Additional file : Table S1). The extracted sequences were aligned using Muscle [] and manually edited with BioEdit []. Phylogenetic relationships among them were estimated using maximum likelihood and Bayesian approaches. We run maximum likelihood analyses in IQ-Tree ver 1.5.5 [] as implemented in the IQ-Tree web server [] last accessed on June 2017 and evaluated support for the nodes with the ultrafast bootstrap method []. We run Bayesian analyses in MrBayes version 3.2 [], setting four simultaneous chains for 2 × 107 generations, sampling trees every 1000 generations, and using default priors. We assessed convergence by measuring the standard deviation of the split frequency among parallel chains. We summarized results with a majority-rule consensus of trees collected after convergence was reached. […]

Pipeline specifications

Software tools MUSCLE, BioEdit, IQ-TREE, MrBayes
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Caenorhabditis elegans