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est-sfs implements a maximum likelihood method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities for DNA sequence data. The uSFS is a vector of counts of nucleotide sites with x derived allele copies in a sample of gene copies from a population. est-sfs infers the uSFS and ancestral state probabilities at polymorphic sites in a focal species using information from up to three outgroup species. Three models of nucleotide substitution have been implemented. For details of the method, see Keightley and Jackson, Genetics 209: 897-906 (2018).
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