Relationships among prasinophyte lineages inferred using a data set of 14,382 positions assembled from 71 cpDNA-encoded proteins of 47 green plant taxa. Trees were inferred using PhyloBayes under the CATGTR + Γ4 model and RAxML under the LG4X and gcpREV + Γ4 models. In the ML analyses, the data set was partitioned by gene, with the model applied to each of the 71 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 CATGTR + Γ4 analyses, the PP values for the CATGTR + Γ4 analyses, and the BP values for the LG4X and gcpREV + 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 histograms on the left indicate the proportion of missing genes and missing sites for each taxon. The scale bar denotes the estimated number of amino acid substitutions per site.