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"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (Amber) and a package of molecular simulation programs which includes source code and demos (AmberTools).

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between genetic sequences, comparing nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

ClustalW2, ClustallW, and ClustalX are general purpose, multiple sequence alignment tools. Multiple alignments of protein sequences can identify conserved sequence regions. This is useful in designing experiments to test and modify the function of specific proteins, in predicting the function and structure of proteins and in identifying new members of protein families. Clustal is a general purpose multiple sequence alignment program for DNA or proteins.

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