\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio.Emboss.Applications} \PYG{k+kn}{import} \PYG{n}{NeedleCommandline}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{needle\PYGZus{}cline} \PYG{o}{=} \PYG{n}{NeedleCommandline}\PYG{p}{(}\PYG{n}{asequence}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}alpha.faa\PYGZdq{}}\PYG{p}{,} \PYG{n}{bsequence}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}beta.faa\PYGZdq{}}\PYG{p}{,}
\PYG{g+gp}{... }                                 \PYG{n}{gapopen}\PYG{o}{=}\PYG{l+m+mi}{10}\PYG{p}{,} \PYG{n}{gapextend}\PYG{o}{=}\PYG{l+m+mf}{0.5}\PYG{p}{,} \PYG{n}{outfile}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}needle.txt\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{needle\PYGZus{}cline}\PYG{p}{)}
\PYG{g+go}{needle \PYGZhy{}outfile=needle.txt \PYGZhy{}asequence=alpha.faa \PYGZhy{}bsequence=beta.faa \PYGZhy{}gapopen=10 \PYGZhy{}gapextend=0.5}
\end{Verbatim}
