Computational protocol: A deuterostome origin of the Spemann organiser suggested by Nodal and ADMPs functions in Echinoderms

Similar protocols

Protocol publication

[…] Sequences were retrieved from various databases using blast search or keyword search and aligned using Clustal Omega (www.clustal.org/omega/) with default parameters. Alignment was manually checked for obvious errors using Aliview (www.ormbunkar.se/aliview/) then trimmed using Trimalv1.3 (trimal.cgenomics.org/) with user defined parameters (Min. percentage position to conserve: 18, Gap threshold: 0.7, Similarity threshold: 0, Window size: 1). Bayesian phylogenetic analysis was done using MrBayes 3.2.5, mrbayes.sourceforge.net/) with a mixed amino-acid substitution model, and 5 millions generations. Consensus tree was generated after discarding 25% generations as burn-in. […]

Pipeline specifications

Software tools Clustal Omega, AliView, trimAl, MrBayes
Application Phylogenetics