Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences
Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences
Modeling of sequence evolution is fundamental to ancestral sequence reconstruction. Care must be taken in choosing a model, however, as the use of unrealistic models can lead to erroneous conclusions. The choice of model and the effects of assumptions inherent within are discussed in this chapter in terms of their effects on probabilistic ancestral sequence reconstruction. This chapter discusses standard probabilistic models, site rate variation to these models, and deviations from the standard (homogeneous, stationary, reversible) models. Model selection, selecting one model from many, given data, and the comparison of different models are included as well as covarion models, the use of outside information when modeling, and the treatment of gaps.
Keywords: parsimony, likelihood, models, gaps, rate variation, covarion, branch lengths, protein structure
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