Computational protocol: Regulation of chloroplast and nucleomorph replication by the cell cycle in the cryptophyte Guillardia theta

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Protocol publication

[…] The amino acid sequences of G. theta histone H2A were obtained from the JGI portal website (http://genome.jgi.doe.gov/Guith1/Guith1.home.html). The signal peptide cleavage site was predicted by SignalP 3.0. The 41 H2A amino acid sequences were aligned and the poorly aligned regions were eliminated according to Hirakawa et al., except for the following, a setting of Gblocks was applied; half of the gapped positions allowed, the minimum number of a conserved and a flank positions set to 30% and 28% of the number of taxa plus one, respectively. The aligned sequences were calculated using RAxML v8.0.0 with an LG + GAMMA model selected by Aminosan, and the corresponding bootstrap support values were calculated through ML analysis of 1,000 pseudoreplicates. Bayesian analysis was performed with MrBayes5D using an LG + GAMMA model. Markov chain Monte Carlo iterations were carried out until 20,000,000 generations were attained. Trees were sampled every 100 generations. The first 200,000 generations were discarded as burn-in. Posterior probabilities were calculated from all of the post burn-in trees. […]

Pipeline specifications

Software tools SignalP, Gblocks, RAxML
Application Phylogenetics
Organisms Guillardia theta