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Table 2 Description of the five methods considered in the experiment

From: Aligning coding sequences with frameshift extension penalties

Method Alignment approach and specific parameters FS initiation cost Other parameters
fse Present approach \({\texttt{fs}}\_{\texttt{extend}}\_{\texttt{cost}} =\)  \(\,-1; -0.5; -0.2\) \({\texttt{fs}}\_{\texttt{open}}\_{\texttt{cost}} =\) −10; −20; −30 \({\texttt{AA}} \quad {\texttt{gap}}\_{\texttt{open}}\_{\texttt{cost}} = -11\) \({\texttt{AA}} \quad {\texttt{gap}}\_{\texttt{cost}} = -1\) \(s_{aa} =\,{\texttt{BLOSUM62}} \quad {\texttt{matrix}}\) \(s_{an} =\,\) +1/-1 match/mismatch
fse0 Present approach \({\texttt{fs}}\_{\texttt{extend}}\_{\texttt{cost}} = 0\)
macse_p Ranwez et al. [18] \({\texttt{stop}}\_{\texttt{cost}} = -100\)
needleprot NW [24] at AA level Not applicable
needlenuc NW [24] at NT level Not applicable \({\texttt{NT}} \quad {\texttt{gap}}\_{\texttt{open}}\_{\texttt{cost}} = -5\)
\({\texttt{NT}} \quad {\texttt{gap}}\_{\texttt{cost}} = -2\)
\(s_{an} =\) +2/-3
match/mismatch
  1. For each method, the alignment approach and the values of specific and common parameters are given