Best tree from maximum likelihood analysis (Treefinder, mtZoa+G+I) with the 30 taxa dataset (concatenated amino acid alignments). Numbers next to nodes reflect edge support percentage (= LR-ELW) from Treefinder with mtZoa+G+I model (left or upper number), edge support percentage from Treefinder with mtRev+G+I model (middle number) and Bayesian posterior probability (BPP, mtRev+G+I, right or lower number). In the best tree of Treefinder with mtRev+G+I model Myzostoma clustered with Ectoprocta (edge support: 51%). The best tree from Bayesian analysis favoured another topology: Nemertea are sister group to Phoronida+Entoprocta (BPP: 1.0) and Myzostoma clustered with Ectoprocta (BPP: 1.0). Thick lines for clades indicate a combination of edge support above 85% and BPP above 0.95. Scale bar depicts substitutions per site. For complete species names and GenBank accession numbers see Additional file 1. Asterisks indicate taxa with incomplete mt genome records.