Figure 3.

ValRS trees obtained with the ML method of protein phylogeny (JTT-F model). See also the legend of Fig. 2. Asterisks (★) denote amitochondriate eukaryotes. @, Putative gene duplication (see Results). Unambiguously aligned 555 positions were selected and used. These correspond to the following positions in the ValRS sequence of G. lamblia: 61–82, 97–143, 145–153, 166–253, 358–393, 402–406, 409–452, 469–531, 554–581, 624–645, 657–683, 686–720, 760–801, 892–940, 968–990, 1002–1009, and 1067–1073. (A) A ProtML tree finally selected by the local rearrangement method of the protml program. (B) A ProtML tree estimated on the basis of the QP topology.