I've been asked to analyze a very large dataset of DNA barcodes (short 600-ish bp COI gene sequences) to compare INTERspecific vs. INTRAspecific sequence distances. I've had some luck using fdnadist (the EMBOSS version of Phylip's dnadist) and the APE package in R to generate distance matrices, and then parsing the output. Unfortunately, as the number of sequences grows, the generation of distance matrices becomes memory-prohibitive. I'm looking for a way to loop through the set of sequences and compute distance measures on the fly, and store these numbers either in a database or text file, to avoid the memory problem.
Is there a good tool that can generate this distance measure between 2 DNA sequences?