Public Domain Programs & Tools

Tools include

• phred - used to read chromatograms, extract sequence & qual scores. Does signal processing, compares peaks associated with each dye/base, spacing, etc.
• phrap -- used to align 2 or more seqs, using qual score data, if available. Both phred & phrap are from Phil Green, Wash U
• BLAST -- Basic Linear Alignment Search Tool (NCBI) - provides alignments & statistical measures
• FASTA/FASTX - Alignment programs for DNA/DNA or DNA/peptide, from Bill Pierson, UVa
• sim4, fgenes, genscan -- gene finding on full genomic sequences
• many others

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