seqalignviewer

R2026b

Visualize multiple sequence alignment

Syntax

seqalignviewer

seqalignviewer(Alignment)

seqalignviewer(Alignment,Name=Value)

Description

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

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

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

Examples

View a Multiple Sequence Alignment File

Load and view a multiple sequence alignment file.

seqalignviewer('aagag.aln')

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

Alignment — Multiple sequence alignment (MSA) data

structure | character array | character vector | string vector | 3-by-N character array

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.

Example: seqalignviewer(Alignment,Alphabet="AA") specifies that the aligned sequences are amino acid sequences.

Alphabet — Type of aligned sequences

'AA' | 'NT'

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'

SeqHeaders — List of names to label sequences in alignment window

array of structures containing a Header or Name field | cell array of character vectors | string vector

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

R2026b: Updated app for viewing sequence alignments

Use the updated Sequence Alignment app to inspect sequence alignments, view the consensus sequence information, export consensus or alignments to a file or MATLAB workspace, and generate a phylogenetic tree from aligned sequences.

R2026b: Manual editing of sequence alignments removed

You can no longer edit sequence alignments manually in the app. Instead, use alignment functions, such as multialign, nwalign, and swalign, to perform sequence alignments programmatically.

R2017b: 'R2012b' option in seqalignviewer has been removed

The 'R2012b' name-value pair has been removed. The default version of seqalignviewer runs more robustly than the previous version (R2012b).