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Figure 8 | BMC Evolutionary Biology

Figure 8

From: Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences

Figure 8

Pseudogenes: Influence of root sequence distributions on model fit (against independence throughout the entire tree) using independent model frequencies. Various orders of Markov chains for the ancestral root sequence are tested against the assumption of site-independent evolution throughout the entire tree, revealing that a second-order Markov chain yields the largest increase in model fit vis-à-vis the independent GTR model. The first model comparison (of which the order is indicated by '-') does not assume a separate Markov chain at the ancestral root but uses the independent model frequencies to describe the ancestral root sequence. Both annealing and melting schemes are shown for each model comparison, as well as 95% confidence intervals for both schemes.

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