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2.3.1.8 Counts of parsimony informative sites for a species quartet

The FourSpeciesSitePatternCounts computes the frequency of each type of informative sites. With four species, 3 types are expected: 1100, 0110 and 1010. On entry will be output for each of these types. The remaining sites will be pulled in a column called “Ignored”.

Synopsis:

maf.filter=                                 \
    [...],                                   
    SequenceStatistics(                     \
        statistics=(\                       \
            [...],                                                    
            FourSpeciesSitePatternCounts(   \
                species1=sp1,               \
                species2=sp2,               \
                species3=sp3,               \
                species4=sp4                \
            [...]),                         \
        ref_species=sp1,                    \
        file=data.statistics.csv),          \
    [...]

Arguments:

species1=species

First species to consider (resp. second, third and fourth).