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mafft_site_score

Source: R/mafft_native.R
mafft_site_score.Rd

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

Usage

mafft_site_score(M, ga, gb, wa, wb, i, j)

Arguments

M

Passed to mafft_lookup.

ga

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

gb

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

wa

A vector; indexed elementwise.

wb

A vector; indexed elementwise.

i

Character; passed to substr.

j

Character; passed to substr.

Value

The value of tot, as built in the body.

Examples

sc <- normalized_similarity_matrix(seq_type = "aa")
mafft_site_score(sc$M, list("MKV"), list("MRV"), 1, 1, 2L, 2L)
#> [1] 0