pairwiseEqual determined pairwise equivalence between a pairs in a set of sequences, excluding ambiguous positions (Ns and gaps).
pairwiseEqual
pairwiseEqual(seq)
character vector containing a DNA sequences.
A logical matrix of equivalence between each entry in seq. Values are TRUE when sequences are equivalent and FALSE when they are not.
seq
TRUE
FALSE
Uses seqEqual for testing equivalence between pairs. See pairwiseDist for generating a sequence distance matrix.
# NOT RUN { # Gaps and Ns will match any character seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C", E="NTGGG") d <- pairwiseEqual(seq) rownames(d) <- colnames(d) <- seq d # }
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