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Sequence Alignment

Visualize and edit multiple sequence alignments


The Sequence Alignment app lets you visualize and edit multiple sequence alignments.

You can:

  • Inspect the sequence alignment and make manual adjustments.

  • View the consequence sequence information and export it to a file or MATLAB® workspace.

  • Generate a phylogenetic tree from aligned sequences.

Sequence Alignment app

Open the Sequence Alignment App

  • MATLAB Toolstrip: On the Apps tab, under Computational Biology, click the app icon.

  • MATLAB command prompt: Enter seqalignviewer.


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Load and view a multiple sequence alignment file.


Figure Biological Sequence Alignment - 1 contains 3 axes objects and other objects of type uipanel, uitoolbar, uimenu. Axes object 1 contains 2 objects of type text, patch. Axes object 2 contains 5 objects of type image, text, patch. Axes object 3 contains 6 objects of type image, patch, text.

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 .

Related Examples

Programmatic Use

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seqalignviewer opens the Sequence Alignment app.

seqalignviewer(Alignment) loads multiple sequence alignment data Alignment into the app. Alignment can be one of the following:

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

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

  • A string specifying a file or URL that contains MSA data

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

seqalignviewer('close') closes the app.

Version History

Introduced in R2012b