Additional file 3: of A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

Phylogenies inferred from 47 individual proteins. Consensus alignments of orthologous sequences of 47 proteins retrieved from 14 amoebozoan genomes were determined using M-coffee, with eight alignment algorithms. Regions with poor consensus alignment or with long insertions in only few proteins were deleted. Phylogenies were inferred by Bayesian inference using a mixed amino-acid substitution models with rate variation between sites estimated by a gamma distribution with a proportion of invariable sites. Analysis were run for one million generations. Trees were rooted at midpoint using Figtree ( http://tree.bio.ed.ac.uk/software/figtree/ ), with posterior probabilities shown at the nodes. Panel A: proteins a-h; Panel B: proteins m-x. The consensus phylogeny of all 47 concatenated proteins (see also Fig. 2) is shown top left in Panel A. (PDF 156 kb)