MafFilter Manual 1.3.1: PairwiseDivergence

2.3.1.6 Pairwise divergence

The PairwiseDivergence computes the divergence (percentage of mistmatch) between two species. If at least one of the species is missing, NaN is returned. It will send an error however if the block has more than one sequence for this species (be sure to use the Subset filter before, if needed).

Synopsis:

maf.filter=                                 \
    [...],                                   
    SequenceStatistics(                     \
        statistics=(\                       \
            [...],                                                    
            PairwiseDivergence(             \
                species1=species1,          \
                species2=species1),         \
            [...]),                         \
        ref_species=species1,               \
        file=data.statistics.csv),          \
    [...]

Arguments:

species1={string}: The first species for which divergence should be reported.
species2={string}: The second species for which divergence should be reported.