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# Table 2 Description of the five methods considered in the experiment

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.  $${\texttt{stop}}\_{\texttt{cost}} = -100$$
needleprot NW  at AA level Not applicable
needlenuc NW  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 