You may use the CONTRAlign server to perform sequence alignments. Input to the server consists of 2 FASTA format sequences, each up to 2000 characters in length.

For larger alignments, CONTRAlign may be executed on your local machine (see download page). (See the FAQ for a note regarding multiple alignments with CONTRAlign.)

The email server is currently down. Please use the web interface.

Step 1: Choose either of two input methods.

(a) Enter FASTA format sequences (see example)


(b) Upload FASTA format text file:

Step 2: Choose either of two output methods.

Send results to e-mail address:

Type your e-mail address:  
Re-type your e-mail address:  


Send results to web browser.

Step 3: Click submit!