Statistical Alignment of Retropseudogenes and Their Functional Paralogs

We describe a model for the sequence evolution of a processed pseudogene and its paralog from a common protein-coding ancestor. The model accounts for substitutions, insertions and deletions, and combines nucleotide- and codon-level mutation models. We give a dynamic programming method for calculating the likelihood of homology between two sequences in the model, and describe the accompanying alignment algo-rithm. We also describe how ancestral codons can be computed when the same gene produced multiple pseudogene homologs. We apply our methods to the evolution of human cytochrome c. Key words molecular evolution, pairwise sequence alignment, processed pseudo-genes, Thorne-Kishino-Felsenstein model, cytochrome c. Running title Statistical alignment of retropseudogene