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(___,'R2012b',true) runs the previous version of the Sequence Alignment app, using any of the input arguments in previous syntaxes.
This example shows how to view a multiple sequence alignment file.
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.
Multiple sequence alignment (MSA) data, specified as:
MATLAB character array containing MSA data, such as returned by multialign
String specifying a file or URL containing MSA data
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.
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'.
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 strings. The number of elements in either array must be the same as the number of sequences in the alignment data Alignment.
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.