Service Retirement

We remind you that it is not long until the EBI's Wise2DBA and Promoterwise services are retired on 15th April 2018. Alternatives can be found at Exonerate, BWA or BLAT. If you have any concerns, please contact us via support.



A fast and accurate multiple sequence alignment algorithm.

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How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Sequence

Sequence Input Window

Three or more sequences to be aligned can be entered directly into this form. Sequences can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is currently a sequence input limit of 2000 sequences and 2MB of data.

Sequence File Upload

A file containing three or more valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be uploaded and used as input for the multiple sequence alignment. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters. There is currently a file upload limit of 2000 sequences and 2MB of data.

Sequence Type

Indicates if the sequences to align are protein or nucleotide (DNA/RNA).

Type Abbreviation
Protein protein
Nucleic Acid dna

Default value is: Protein [protein]

STEP 2 - Set your Parameters

Output Format

Format for generated multiple sequence alignment.

Output Format Description Abbreviation
Pearson/FASTA Pearson or FASTA sequence format fasta
ClustalW ClustalW alignment format without base/residue numbering clu
MACSIM Macsim XML alignment format macsim

Default value is: ClustalW [clu]

Gap Open

The penalty for opening/closing a gap. Half the value will be subtracted from the alignment score when opening, and half when closing a gap.

Default value is: 11.0

Gap Extension

Penalty for extending a gap

Default value is: 0.85

Terminal Gap

Penalty to extend gaps from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences

Default value is: 0.45

Bonus Score

A bonus score that is added to each pair of aligned residues

Default value is: 0.0

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).


Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.
(2008 December 22) Nucleic acids research 37 (3) :858-865
Kalign--an accurate and fast multiple sequence alignment algorithm.
(2005 December 12) BMC bioinformatics 6 :298
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
Analysis Tool Web Services from the EMBL-EBI.
(2013 May 13) Nucleic acids research 41 (Web Server issue) :W597-600