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.