BioSeqAnalyzer is a bioinformatics software tool for analyzing DNA and protein sequences.    
Its Windows interface makes sequence analysis extremely easy.  
BioSeqAnalyzer, registered version, supports the following 
operations: 
    Alignment Scoring. 
    Linear global alignment. 
    Affine global alignment.  
    Local alignment. 
    Multiple alignment. 
    Hidden Markov Models Profile creation. 
    Aligning to Hidden Markov Models Profiles. 
    Composition-based classification. 
    Profile-based classification. 
All functions can be performed on both DNA and protein sequences. 
BioSeqAnalyzer brings to sequence analysis the following GUI features: 
    Enter sequences either from the keyboard or from FASTA files. 
    Select a FASTA file from a list of previously-used files. 
    Select a sequence from within a multi-sequence FASTA file using a simple listbox. 
    Select substitution score matrix with a single click. 
    View alignments in either wide, or wrap-around format. 
    View or hide Dynamic Programming matrices. 
    Create and save HMM profiles. 
    Align sequences to a previous-saved HMM profiles. 
    Much more.