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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”.
maf.filter= \
[...],
SequenceStatistics( \
statistics=(\ \
[...],
FourSpeciesSitePatternCounts( \
species1=sp1, \
species2=sp2, \
species3=sp3, \
species4=sp4 \
[...]), \
ref_species=sp1, \
file=data.statistics.csv), \
[...]
|
species1=speciesFirst species to consider (resp. second, third and fourth).