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MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.

Official Website
Download Software

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, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot 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 500 sequences and 1MB of data.

Sequence File Upload

A file containing three or more valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) 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 500 sequences and 1MB of data.

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 clustalw

Default value is: Pearson/FASTA [fasta]


Protein comparison matrix to be used when adding sequences to the alignment.

Matrix (Protein Only) Description Abbreviation
None none
BLOSUM30 bl30
BLOSUM45 bl45
BLOSUM62 bl62
BLOSUM80 bl80
JTT PAM100 jtt100
JTT PAM200 jtt200

Default value is: BLOSUM62 [bl62]

Gap Open

Penalty for first base/residue in a gap.

Default value is: 1.53

Gap Extension

Penalty for each additional base/residue in a gap.

Default value is: 0.123


The order in which the sequences appear in the final alignment

Order Description Abbreviation
aligned Determined by the guide tree aligned
input Same order as the input sequences input

Default value is: aligned

Tree Rebuilding Number

Tree Rebuilding Number

Default value is: 2

Guide Tree Output

Generate guide tree file

Default value is: ON [true]

Max Iterate

Maximum number of iterations to perform when refining the alignment

Default value is: 2

Perform FFTS

Perform fast fourier transform

Order Description Abbreviation
none none
localpair localpair
genafpair genafpair
globalpair globalpair

Default value is: none

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 joe@example.org 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).


MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
(2013 April) Molecular biology and evolution 30 (4) :772-80
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 July 01) Nucleic acids research 43 (W1) :W580-4
Analysis Tool Web Services from the EMBL-EBI.
(2013 July) Nucleic acids research 41 (Web Server issue) :W597-600