Alignment Analysis
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 Tools    >> Sequence Variability Server


This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function. H values range from 0 (only one residue in present at that position) to 4.3 (all 20 residues are equally represented in that position).

Sequence variability is then plotted against the selection of either consensus sequence, first sequence, or most abundant sequence in the alignment.

In addition, the server allows the user to set a Shannon Filter in order to search the alignment for sequence stretches with variability (Shannon Entropy, H) under the set value. For more detailed information click here

Alignment name:


Upload your alignment file (CLUSTAL format), or

Paste your alignment. Remember in CLUSTAL format

Output Sequence: Consensus sequence:         Threshold: 55% 70% 80% 90%
Most abundant sequence
First sequence in alignment
Shannon Filter:
Shannon Entropy Threshold
Fragment Length

For questions about this site: Pedro A. Reche


Shannon Entropy calculations Rob Meijers

Shannon filter and web programming by Pedro A. Reche

Hits since June/2002 Last updated:
This tool is also available at this site

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