MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing differen...
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the a...
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. It attempts to calculate the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
www.clustal.org/clustal2
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