Module bio::stats::pairhmm

A pair Hidden Markov Model for calculating the probability that two sequences are related to each other. Depending on the used parameters, this can, e.g., be used to calculate the probability that a certain sequencing read comes from a given position in a reference genome.

Structs

PairHMM

A pair Hidden Markov Model for comparing sequences x and y as described by Durbin, R., Eddy, S., Krogh, A., & Mitchison, G. (1998). Biological Sequence Analysis. Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.

Enums

XYEmission

Traits

EmissionParameters	Trait for parametrization of PairHMM emission behavior.
GapParameters	Trait for parametrization of PairHMM gap behavior.
StartEndGapParameters	Trait for parametrization of PairHMM start and end gap behavior. This trait can be used to implement global and semiglobal alignments.