We implemented a pair HMM with 10 non-silent states match/mistmatch state in V gene, insertion in V gene (Iv), deletion in V gene (Dv), V D junction n nucleotides, match/mismatch in DH gene, insertion in the DH gene (Id), deletion in the DH gene (Dd), D J junction n nucleotides, match/mismatch in the J gene, insertion in the J gene (Ij) and deletion in the J gene (Dj).
We implemented a paired climbed-unclimbed design that successfully removed potentially confounding environmental variation.
Another example, MorphMS, implemented a pair-HMM statistical alignment between two species [42].
This is unsurprising because, to the authors' knowledge, AdapterRemoval is the only other tool to implement a pair-aware adapter removal strategy.
Although the pedigree structures are uncomplicated and the underlying genetic principles straightforward, a surprising degree of complexity is involved in implementing a sib pair study and interpreting the results.
We used a previously developed active-learning exercise in which students assign playing cards randomly into two groups (Enders et al., 2006) and extended this exercise to have students physically implement a matched-pair design using playing cards.
To check if the observed differences can be expected as a general outcome when comparing deterministic and stochastic methods for this problem, we implement an additional pair of methods.
The beam scanning was implemented by a pair of high speed galvanometer mirrors controlled by a function generator and a data acquisition (DAQ) card.
The laser beam scanning was implemented using a pair of galvanometer mirrors controlled by an analog output card PXI-62599, National Instrument), where the fast-axis sweep was driven by the FBG A-scan trigger and the slow-axis sweep was controlled by the software.
To analyse all the study subjects without having to remove one of each kin pair, we considered implementing a mixed-regression association analysis in which phenotypic correlation was proportional to K [38], [39], while age and sex were fitted as fixed effects.
