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Visualize and edit multiple sequence alignment



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.


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

  • Character array or column vector of strings 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 Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

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

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, cell array of character vectors, or string vector. The number of elements in either array must be the same as the number of sequences in the alignment data Alignment.

Example: 'SeqHeaders',names

Version History

Introduced in R2012b

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