Computational protocol: Development of the larval anterior neurogenic domains of Terebratalia transversa (Brachiopoda) provides insights into the diversification of larval apical organs and the spiralian nervous system

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Protocol publication

[…] The deduced amino acid sequences for Terebratalia forebrain embryonic zinc-finger, Forkhead G, orthopedia, otx, NK2.1, homeobrain, synaptotagmin 1, and Six3/6 along with those for representative related proteins from other taxa, retrieved from NCBI (html://http://ncbi.nlm.nih.gov/; accession numbers listed below) and Joint Genome Institute (http://genome.jgi-psf.org/Capca1/Capca1.home.html for Capitella teleta; http://genome.jgi-psf.org/Lotgi1/Lotgi1.home.html for Lottia gigantea; http://genome.jgi-psf.org/Nemve1/Nemve1.home.html for Nematostella vectensis; http://genome.jgi-psf.org/Triad1/Triad1.home.html for Trichoplax adhaerens; protein ID numbers listed below), were aligned with MUSCLE [] or MacVector. The resulting alignments of conserved domains were corrected by eye. For each dataset, Bayesian phylogenetic analysis was performed using a parallelized version of MrBayes [,], with four independent runs and a mixed model of protein evolution. Each analysis was run until the average standard deviation of split frequencies between runs was less than 0.01 (10,000,000 generations for fez, NK-class, Paired-class, Six-class and Synaptotagmin datasets; 20,000,000 generations for the Fox-class dataset). A consensus tree and posterior probabilities for each node were calculated from the final 2,000,000 generations of each run. For all accession numbers and protein sequences used in phylogenetic analyses see additional files. […]

Pipeline specifications

Software tools MUSCLE, MacVector, MrBayes
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Terebratalia transversa