Get the frequencies of characters in an alignment
base.freq.msa(x, seq = NULL, ignore.missing = TRUE, ignore.gaps = TRUE)An object of type msa
A vector of character strings identifying the sequence(s)
to get base frequencies for. If NULL, use all sequences.
If TRUE, ignore missing data characters ("N" and "?"). Must be TRUE if seq is stored as a pointer.
If TRUE, ignore gaps. Must be TRUE if seq is stored as a pointer.
A data frame with one row for each unique state (usually "A", "C", "G", "T", and possibly "N", "?", "-", counts for each state, and overall frequency of each state.
statfreq.msa, which gets observed frequencies of states
in an alignment with respect to a substitution model, and works for
pointers.