\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio.Align.Applications} \PYG{k+kn}{import} \PYG{n}{MuscleCommandline}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{cline} \PYG{o}{=} \PYG{n}{MuscleCommandline}\PYG{p}{(}\PYG{n+nb}{input}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}opuntia.fasta\PYGZdq{}}\PYG{p}{,} \PYG{n}{out}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}opuntia.aln\PYGZdq{}}\PYG{p}{,} \PYG{n}{clwstrict}\PYG{o}{=}\PYG{k+kc}{True}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{cline}\PYG{p}{)}
\PYG{g+go}{muscle \PYGZhy{}in opuntia.fasta \PYGZhy{}out opuntia.aln \PYGZhy{}clwstrict}
\end{Verbatim}
