Public Domain Programs & Tools
- phred - used to read chromatograms, extract sequence & qual scores.
Does signal processing, compares peaks associated with each dye/base,
- 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 &
- 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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