>>> from Bio.Align.Applications import MuscleCommandline
>>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.txt")
>>> print cline

默认情况下，MUSCLE的输出文件将是包含间隔（gap）的FASTA格式文件。你也可以告诉MUSCLE来输出ClustalW-like的文件结果：
>>> from Bio.Align.Applications import MuscleCommandline
>>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clw=True)
>>> print cline

严格的ClustalW的输出文件：
>>> from Bio.Align.Applications import MuscleCommandline
>>> cline = MuscleCommandline(input="opuntia.fasta", out="opuntia.aln", clwstrict=True)
>>> print cline

大佬，我的fasta文件要放在哪个路径下才能运行啊