This document is for OpenStructure version 1.6, the latest version is 2.7 !

clustalw - Perform multiple sequence alignment

ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=False, clustalw_option_string=False)

Runs a clustalw multiple sequence alignment. The results are returned as a AlignmentHandle instance.

There are two ways to use this function:

  • align exactly two sequences:

    param seq1:sequence_one
    type seq1:SequenceHandle or str
    param seq2:sequence_two
    type seq2:SequenceHandle or str

    The two sequences can be specified as two separate function parameters (seq1, seq2). The type of both parameters can be either SequenceHandle or str, but must be the same for both parameters.

  • align two or more sequences:

    param seq1:sequence_list
    type seq1:SequenceList
    param seq2:must be None

    Two or more sequences can be specified by using a SequenceList. It is then passed as the first function parameter (seq1). The second parameter (seq2) must be None.


Note: ClustalW will convert lowercase to uppercase, and change all ‘.’ to ‘-‘. OST will convert and ‘?’ to ‘X’ before aligning sequences with Clustalw.

ClustalW will accept only IUB/IUPAC amino acid and nucleic acid codes:

Residue Name Residue Name
A alanine P proline
B aspartate or asparagine Q glutamine
C cystine R arginine
D aspartate S serine
E glutamate T threonine
F phenylalanine U selenocysteine
G glycine V valine
H histidine W tryptophan
I isoleucine Y tyrosine
K lysine Z glutamate or glutamine
L leucine X any
M methionine * translation stop
N asparagine - gap of indeterminate length


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Documentation is available for the following OpenStructure versions:

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If something is missing or if you need the C++ API description in doxygen style, check our old documentation for further information.