MaxAlike algorithm aims at reconstructing a nucleotide sequence in a target species, based on a multiple sequence alignment and a phylogenetic tree of homologous sequences from other species. For each alignment position the probabilities of occurrence for each nucleotide are computed, considering the phylogenetic position of the target species in the tree.
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P. Menzel, P. F. Stadler and J. Gorodkin:
maxAlike: Maximum-likelihood based sequence reconstruction with application to improved primer design for unknown sequences,
Bioinformatics, 2011, 27, 317-325.