Nomad

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.