Supplementary data files for "Archaeal 'dark matter' and the origin of eukaryotes"

<p>This is the supplementary data file associated with Williams and Embley (2014) GBE "Archaeal 'dark matter' and the origin of eukaryotes". It includes the alignments and tree files generated as part of the analysis.</p

Phylogeny based on 24 mitochondrial/bacterial proteins (6,542 amino acid positions) inferred by Bayesian Inference with the WAG + F (left) or the CAT mixture (right) model.

<p>Numbers indicate posterior probability values. Branches without values are supported by posterior probabilities of 1.0. The scale bar denotes the estimated number of amino acid substitution per site. See supplementary material for complete species names and proteins used.</p

Phylogeny based on 24 mitochondrial/bacterial proteins (6,542 amino acid positions) inferred by Bayesian Inference with the WAG/GTR + F (left) or the CAT mixture (right) model on the non recoded and Dayhoff recoded dataset.

<p>(see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030520#s3" target="_blank">Methods</a> for details). Branches without values are supported by posterior probabilities of 1.0. When at least one dataset gives posterior probability <1, both values are shown, standard coding on the left and Dayhoff coding on the right. The scale bar denotes the estimated number of amino acid substitution per site. See supplementary material for complete species names and proteins used.</p

Phylogeny based on 24 mitochondrial/bacterial proteins (6,542 amino acid positions) inferred by Bayesian Inference with the GTR + F (left) or the CAT mixture (right) model on the Dayhoff recoded dataset.

<p>(see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030520#s3" target="_blank">Methods</a> for details). Branches without values are supported by posterior probabilities of 1.0. The scale bar denotes the estimated number of amino acid substitution per site. See supplementary material for complete species names and proteins used.</p

Nucleotide and amino acid composition of the dataset used in this study.

<p>A) Bar graph displaying the percentage of A+T in the concatenation of the nucleotide sequences. B) Reduced dimensionality plot showing the main principal components of the global amino acid compositions. Dots are coloured as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030520#pone-0030520-g001" target="_blank">Figure 1A</a>. The group of overlapping dots at the bottom right corner contains the species with the lowest A+T %. The variances that explain the two first axes are respectively 92.3% and 6.3%.</p

Sequences, alignment and Newick tree file for NTT phylogeny

<p>This archive contains the raw NTT sequence alignment, masked sequence alignment, and Newick tree from an analysis of the alignment under the C20 model in PhyloBayes 3.3. </p

29_alns_cut.tar

The genes used to make the 29BAE dataset, after masking of poorly-aligning and uninformative sites

64_singles.tar

The genes used to make the 64AE dataset, after masking of poorly-aligning and uninformative sites

29_aeb

Concatenation of 29 genes conserved in Bacteria, Archaea and eukaryotes

aeb_fasta_files.tar

Single genes conserved between Bacteria, Archaea and eukaryotes. These are the "raw" fasta files, before alignment editing