clustal

Clustal, Multiple alignment of nucleic acid and protein sequences. official website: http://www.clustal.org/

使用biopython, 有相应的接口可以直接调用clustalw.

from Bio.Align.Applications import ClustalwCommandline

# the path of clustalw
clustalw_exe = r'clustalw2.exe'
# the command of clustalw
clustalw_cline = ClustalwCommandline(clustalw_exe, infile=pairFile)
# run the command
stdout, stderr = clustalw_cline()

结果会直接生成aln文件，名字和infile名字一样，后缀为aln。

也可以直接使用biopython中的接口解析结果文件。

from Bio import AlignIO
align = AlignIO.read("opuntia.aln", "clustal")
print align