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Nomad tool

Documentation is available
Nomad (Neighborhood Optimization for Multiple Alignment Discovery) is a program dedicated to the ungapped local multiple alignment (ULMA) problem, also known as "blocks". By using an entropy-based objective function that takes into account the amino acid's nature, Nomad is well suited to deal with protein sequences. This objective function, the shared entropy, has been shown to be significantly more reliable than the relative entropy when protein sequences to be aligned are distantly related.
Please fill out the following form, then press the Run Nomad button.

Paste FASTA sequences:
Or upload file

Sequences type:

Width of the alignment

Occurrences distribution constrains (see documentation):

Total number of occurences (required for the ALOOPS, AMOOPS and AOPS constrains)

sort the occurrences by the log-odd score

Your e-mail address (to get the results by e-mail)