Outline of the information flow of jpHMM. As input, jpHMM expects an MSA partitioned into subtypes as well as an (unaligned) query sequence. Furthermore, the model parameters, based on which different details of the underlying model are determined, have to be set by the user. That is, the emission and transition probabilities and certain parts of the topology of the model are set based on the parameters. jpHMM then derives the most probable path through its pHMMs. As output, jpHMM assigns each position of the query sequence to a subtype of the MSA. Here, three possible outputs are shown.