2.3.1.7 Site statistics

SiteStatistics computes site-wise statistics, including:

• Number of sites without gap,
• Number of complete sites (no gap, no unresolved character),
• Number of complete sites with only one state (constant sites),
• Number of complete sites with only two states (biallelic sites),
• Number of complete sites with only three states (triallelic sites),
• Number of complete sites with all four states (quadriallelic sites),
• Number of parsimony-informative sites.

The statistics are computed for a given subset of species (typically forming a ingroup).

Synopsis:

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

Arguments:

species={list}

A list of species to be considered in the statistics calculations.