Protocol Informatics Component Framework
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Input
    - Pcap file
    - Newline delimited ASCII file

Classification
    - Entropic edit distance
    - Stochastic grammar comparison
    - Local alignment scoring

Sequence Alignment
    - Needleman Wunsch (global)
    - Smith Waterman (local)
    - HMM (global)

Similarity Matrices
    - Binary protocol matrix
    - Plaintext protocol matrix (english)
    - Mixed mode protocol matrix

Splice Site Prediction
    - Consensus gapped and ungapped
    - HMM profile

Phylogenetic Tree Construction
    - UGPMA
    - Maximum parsimony
    - Maximum likelihood

Data Presentation
    - Histogram consisting of mutation rate and composition
    - Color-Coded alignment