Phylogenomic relationships of ciliates. ML tree topology of a phylogenomic matrix comprising 53,873 unambiguously aligned amino acid residues of 27 taxa were inferred by using RAxML software under the LG + F + Γ4 model. Two Plasmodium spp. were used as outgroups. New sequencing species in this study are in red script with yellow shading. Numbers at nodes are ML bootstrap values followed by BI posterior probability. Bootstrap values from 100 replicates are given on the nodes. The scale bar corresponds to 0.1 expected substitutions per site.