Relationships among prasinophyte lineages inferred using a data set of 15,549 positions assembled from 79 cpDNA-encoded proteins of 34 green plant taxa. Trees were inferred using PhyloBayes under the CATGTR + Γ4 model and RAxML under the LG4X, GTR + Γ4 and gcpREV + Γ4 models. In the ML analyses, the data set was partitioned by gene, with the model applied to each of the 79 partitions. The Bayesian majority-rule consensus tree is presented. Support values are reported on the nodes: from top to bottom, or from left to right, are shown the BP values for the LG4X, GTR + Γ4 and gcpREV + Γ4 analyses, and the PP values for the CATGTR + Γ4 analyses. Dashes (−) indicate lower than 0.95 PP or 40% BP support values; black dots indicate that the corresponding nodes received 1.00 PP and 100% BP support values. The scale bar denotes the estimated number of amino acid substitutions per site.