Additional file 10.
Plastid genes supporting the sisterhood of either haptophytes and heterokonts or haptophytes and cryptophytes. The histograms list the genes favoring the given topology over the other according to the codeml amino-acid ML score with the WAG matrix  and gamma distributed rates. The site-specific likelihood values were calculated using parameter estimates and branch lengths based on the concatenated alignment with all the genes. The height of the histogram bars represent the log likelihood preference for the given topology over the other for a particular gene (i.e. the sum of site likelihoods in the concatenated alignment corresponding to a particular gene). (A) The topology found using MrBayes with 21,659 plastid amino-acid positions shared among the chromophytes, Gracilaria, and Porphyra. Invariant sites and gamma distributed rates were used with the Cprev model . The posterior probabilities were 1.0 for all nodes. (B) The topology was found as in (A) except that Guillardia and Emiliania were constrained to be monophyletic. The node corresponding to the chromist clade had a posterior probability of 0.98 and the other nodes had 1.0.
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Rice and Palmer BMC Biology 2006 4:31 doi:10.1186/1741-7007-4-31