In the terms of a typical hidden Markov model, the observed states are the individual alignment columns and the "hidden" states represent the presumed ancestral sequence from which the sequences in the query set are hypothesized to have descended.
Nos termos dun típico modelo oculto de Markov, os estados observados son as columnas individuais do aliñamento, e os estados "ocultos" representan a suposta secuencia ancestral desde a cal se presume que descenden as secuencias do conxunto problema.