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Visualize and edit multiple sequence alignment

'R2012b' name-value pair argument has been removed.





seqalignviewer opens the Sequence Alignment app, where you can display and interactively adjust multiple sequence alignments.

seqalignviewer(Alignment) loads a group of previously multiply aligned sequences into the app, where you can view and interactively adjust the alignment.

seqalignviewer(Alignment,Name,Value) opens the app with additional options specified by one or more Name,Value pair arguments.

seqalignviewer('close') closes the Sequence Alignment app.


If gaps are available after you have selected a block from aligned sequences, then there are three regions that you can drag and move horizontally:

  • Selected block

  • Block on the left of the selection

  • Block on the right of the selection


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Load and view a multiple sequence alignment file.


Alternatively, you can click Sequence Alignment on the Apps tab to open the app, and view the alignment data.

You can also generate a phylogenetic tree from aligned sequences from within the app. Select Display > View Tree .

Input Arguments

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Multiple sequence alignment (MSA) data, specified as:

  • MATLAB® structure containing a Sequence field, such as returned by fastaread, gethmmalignment, multialign, or multialignread

  • MATLAB character array containing MSA data, such as returned by multialign

  • Character vector specifying a file or URL containing MSA data

  • 3-by-N character array showing the pairwise alignment of two sequences, such as returned by nwalign or swalign.

Name-Value Pair Arguments

Specify optional comma-separated pairs of Name,Value arguments. Name is the argument name and Value is the corresponding value. Name must appear inside single quotes (' '). You can specify several name and value pair arguments in any order as Name1,Value1,...,NameN,ValueN.

Example: 'Alphabet','AA' specifies that the aligned sequences are amino acid sequences.

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Type of aligned sequences, specified as 'AA' for amino acid sequences or 'NT' for nucleotide sequences. If you do not specify the type, seqalignviewer attempts to determine the correct type. If it cannot, it defaults to 'AA'.

Example: 'Alphabet','AA'

List of names to label the sequences in the alignment window, specified as a MATLAB array of structures containing a Header or Name field or cell array of character vectors. The number of elements in either array must be the same as the number of sequences in the alignment data Alignment.

Example: 'SeqHeaders',names


You can also display a color-coded multiple or pairwise sequence alignment using the showalignment function. However, the alignment displays in a MATLAB Figure window, where you cannot interact with it.

Introduced in R2012b

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