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PHYLIP and DNADIST

PHYLIP and DNADIST - Microbiology Forum

PHYLIP and DNADIST - Discuss Microbiology Science and Protocols here. Post questions on the study of viruses, fungi, parasites and bacteria here. Microbiology Forum.


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Old 06-30-2007, 02:01 AM
Joe Felsenstein
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Default PHYLIP and DNADIST



In article <[Only registered users see links. ].net>,
Chris Hoffmann <[Only registered users see links. ].upenn.edu> wrote:

1. Dnadist will not add the new distances without recomputing the old ones
in this way.
2. In any case, for the F84 distances the formulas use the base frequencies
found (empirically) in the input sequences. If you add more input
sequences you then most likely have slightly altered empirical frequencies
so you want to recompute the original ones anyway.
3. I suspect our formulas can compute this many distances, but
4. With 20,000 sequences there are 400,000,000 distances in all which, if each
is about 10 bytes long, is a table 4 GB in size. That is too big to
use. You ought to therefore reconsider your motivation for doing this.

I have posted this rather than emailing to the original poster because
it might be educational for others using our programs.

----
Joe Felsenstein [Only registered users see links. ]
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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