Cartoon of a multiple sequence alignment and its mapping to a Markov random field. Shown in the figure is a cartoon figure of a multiple sequence alignment (MSA) and a corresponding Markov random field (MRF). There is one node in the MRF for each column in the MSA. The column-wise conservation statistics in the MSA are encoded by node potentials (Φi). Similarly, the co-variation statistics in the MSA (e.g., between columns 1 and 4) are encoded by edge potentials (φ1,4) in the MRF. The lack of an edge between two nodes means that the corresponding columns are conditionally independent.