is.alignable <- function(a, threshold = .5){
d <- dist.dna(a, model = "raw", pairwise.deletion = TRUE, as.matrix = TRUE)
ub <- list(names(d[, 1])[which(d[, 1] > threshold)],
names(d[, 1])[which(d[, 1] <= threshold)])
ub <- ub[order(sapply(ub, length), decreasing = TRUE)]
length(ub[[2]]) == 0
}
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