Visualize and edit multiple sequence alignment
seqalignviewer opens the Sequence Alignment app, where you
can display and interactively adjust multiple sequence alignments.
seqalignviewer( loads a group
of previously multiply aligned sequences into the app, where you can view and
interactively adjust the alignment.
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:
Block on the left of the selection
Block on the right of the selection
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.
You can also generate a phylogenetic tree from aligned sequences from within the app. Select Display > View Tree .
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
Sequencefield, such as returned by
Character array or column vector of strings containing MSA data, such as returned by
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
Specify optional pairs of arguments as
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.
'Alphabet','AA' specifies that the
aligned sequences are amino acid sequences.
Alphabet — Type of aligned sequences
Type of aligned sequences, specified as
amino acid sequences or
'NT' for nucleotide sequences.
If you do not specify the type,
to determine the correct type. If it cannot, it defaults to
SeqHeaders — List of names to label sequences in alignment window
array of structures containing a
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
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
Version HistoryIntroduced in R2012b
'R2012b' option in
seqalignviewer has been removed
'R2012b' name-value pair has been removed. The default
seqalignviewer runs more robustly than the previous