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Highlighter v1.3.1 (beta)

Purpose: This tool highlights matches and mismatches in a set of amino acid sequences that are aligned and in frame. It is particularly useful for allowing visualization of potential recombination and hypermutation in closely related sequences, such as those isolated from a single patient.

Details: If the "Change Masters" button is not clicked, the first sequence in the file will be taken as the master sequence if aligning against a single master. In case of multiple master sequences (during match), the top n will be chosen as master sequences. For descriptions of options and samples of output, see Highlighter Explanation.

Input
Paste your alignment

[Sample Input]
Or upload sequence file
Ignore alphabet validation
Click to change masters Note: "Match" is the only case in which more than one master can be applied.

Options
Choose what to highlight Mismatches
Matches
Sort sequences by similarity by tree Do not sort
Treat gaps as character? Yes No

Options for Coloring Matches/Mismatches
Color matched/mismatched amino acids by selecting one of the following color schemes:
Standard Se-Al (default) Se-Al (polar/non-polar) BioEdit

Options for Highlighting Matches
The following options apply only if you chose "Matches" above:
Number of masters
Use bars to indicate successive matches? Yes No

last modified: Tue Jan 8 16:05 2013


Questions or comments? Contact us at seq-info@lanl.gov.