Score a simple alignment

Score a simple alignment

score_alignment(
  seq.df,
  seq1,
  seq2,
  sub.mat,
  gap.penalty = -10,
  gap.extend = -4
)

Arguments

seq.df

Two aligned sequences in a dataframe
seq1

name of column with first sequences
seq2

name of column with second sequence
sub.mat

substitution matrix to use. Defaults to BLOSUM62
gap.penalty

penalty for gaps in the sequence
gap.extend

penalty for gap length, starting with the first gap.