Codon-based phylogenetic analyses inferred using CodonPhyml – Yap et al. model [52] for Maximum Likelihood – and MrBayes – GTR substitution model and three categories of non-synonymous/synonymous ratios (M3 model).

<p>Values on the nodes indicate the non-parametric SH test and bootstrap replicates (ML), and posterior probability (BI) support respectively. Where no values are shown on a node, that edge was fully supported under all analyses.</p

Tissue levels of carnitine in human growth. Perspectives in inherited metabolic disases

<p>Phylogenetic relationships within the cnidarian Class Anthozoa according to the “naked corals” (nc) hypothesis (modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094774#pone.0094774-Medina1" target="_blank">[24]</a>).</p

Phylogenetic analyses of the mitochondrial sequences encoding stable RNAs (12S rRNA, 16S rRNA, <i>trnM</i>, and <i>trnW</i>).

<p>Values on the nodes indicate the non-parametric SH test and bootstrap replicates (ML), and posterior probability (BI) support respectively. Where no values are shown on a node, that edge was fully supported under all analyses. Large boxes indicate the Corallimorpharia (dark-gray) and Scleractinia (light-gray) clades. Note that deep-water azooxanthellate species (<i>Corallimorphus profundus</i> and <i>Gardineria hawaiiensis</i>) represent the earliest diverging branches for Corallimorpharia and Scleractinia respectively.</p

Mitochondrial genome sequence data included in the present analyses

<p>Mitochondrial genome sequence data included in the present analyses</p

Comparison of the two competing topologies (scleractinian monophyly, SM, and “naked coral”, NC) using the Approximately Unbiased (AU), Kishino-Hasegawa (KH) and Shimodaira-Hasegawa (SH) tests for a variety of tree reconstruction methods.

<p>The p-values denote the probability that the best ML topology is equivalent to the alternative topologies. Unless otherwise indicated, the trees were based on the alignment of protein coding genes.</p

Codon usage in hexacorallian anthozoans.

<p>CodonW <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094774#pone.0094774-Peden1" target="_blank">[73]</a> was used to estimate codon usage biases; default settings were used in calculation of the codon adaptation index. NC: effective codon number. CAI: codon adaptation index. Colour coding and taxon choice is as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094774#pone-0094774-g002" target="_blank">Figure 2</a>.</p

Posterior probability of the topologies recovered by different models using Phylobayes (SM: scleractinian monophyly, NC: naked coral).

<p>Posterior probability of the topologies recovered by different models using Phylobayes (SM: scleractinian monophyly, NC: naked coral).</p

Phylogenetic analyses based on (a) the nucleotide sequences of the mitochondrial genes encoding proteins and (b) the amino acid sequences of the proteins encoded by the mitochondrial genomes.

<p>Values on the nodes indicate the non-parametric SH test and bootstrap replicates (ML), and posterior probability (BI) support respectively. Where no values are shown on a node, that edge was fully supported under all analyses. Dashed lines indicate the corallimorpharian clade. Light grey blocks identify the scleractinian clades. (I) Octocorallia used as outgroup; (II) Actiniaria; (III) Zoanthidea; (IV) Antipatharia; (V) Corallimorpharia; (VI) “Basal” Scleractinia; (VII) “Robust” Scleractinia; (VIII) “Complex” Scleractinia.</p

Additional file 1. of Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren’s syndrome

Bioinformatics workflow