Sequence Alignment

R2026b

Visualize multiple sequence alignments

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Description

The Sequence Alignment app lets you visualize multiple sequence alignments.

You can:

  • Inspect sequence alignments.

  • View the consensus sequence information.

  • Export consensus or alignments 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.

Examples

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Open Live Script

Load and view a multiple sequence alignment file.

seqalignviewer('aagag.aln')

Figure Biological Sequence Alignment - 1 contains 2 axes objects and other objects of type uigridlayout, uimenu. Axes object 1 contains 6 objects of type image, patch, line. Axes object 2 contains 3 objects of type image, patch.

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

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

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See Also

Apps

Functions