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mafft_nw

Source: R/mafft_native.R
mafft_nw.Rd

A step of the mafft_native implementation. Called by group_align. See the file header for the source the module follows.

Usage

mafft_nw(g1, g2, M, w1, w2, s_op)

Arguments

g1

A vector; its length is taken and its elements indexed.

g2

A vector; its length is taken and its elements indexed.

M

Passed to mafft_site_score.

w1

Passed to mafft_gap_profiles.

w2

Passed to mafft_gap_profiles.

s_op

Numeric; combined arithmetically in the body.

Value

A list with out1, out2.

Examples

sc <- normalized_similarity_matrix(seq_type = "aa")
r <- mafft_nw("MKVLA", "MKLA", sc$M, 1, 1, s_op = -1.53)
unlist(r)
#> out1.MKVLA  out2.MKLA 
#>    "MKVLA"    "-MKLA"