Computational protocol: The evolutionary history of the catenin gene family during metazoan evolution

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Protocol publication

[…] Sequence alignments were performed by ClustalW []. Phylogenetic analysis was carried out using MrBayes 3.1.2 Unix version []. The MPI version of MrBayes was run in parallel on eight nodes with MPICH2 installed []. Bayesian trees with posterior probabilities were constructed with mixed amino acid models, a gamma distribution for rate variation among sites, and a proportion of invariable sites. MrBayes was executed with two runs (four chains for each run), one million generations of Markov Chain Monte Carlo (MCMC) analyses, with 1000 as the sample frequency. The number of MCMC generations indicated convergence of the two runs by having a standard deviation of split frequencies less than 0.05. The posterior probability of each split was estimated by sumt with 250 trees discarded as burnin based on the plot of 'generation vs. log probability'. Parameters were summarized by sump with 250 burnin, and values for the Potential Scale Reduction Factor (PSRF) were all close to 1.0 for all parameters. Bayesian phylogenies with branch lengths and posterior probabilities are shown in Additional files , , , with each tree having sea anemone as the outgroup. Sequence/taxon names in the trees are a combination of gene name, species name, and NCBI sequence identifier. Similar color patterns were applied for species of different phyla as in Figure . For all phylogenies, scale bars represent amino acid replacements per site per unit evolutionary time. The tertiary structures for representative genes were generated by using PyMOL [] (Figure ). [...] Sequence similarity comparisons were conducted by BLAST []. Pairwise distance comparisons were conducted using MEGA4 [] with the Dayhoff model [] and the JTT model []. Statistical significance in the differences between two groups of pairwise distances was evaluated by Wilcoxon rank and Kolmogorov-Smirnov tests implemented in R []. Bayesian trees with posterior probabilities were constructed to determine evolutionary relationships. Functional divergence among homologs was inferred using the DIVERGE software package []. […]

Pipeline specifications

Software tools Clustal W, MrBayes, PyMOL, MEGA, DIVERGE
Applications Phylogenetics, Protein sequence analysis
Organisms Homo sapiens
Diseases Neoplasms