[Molecular-evolution] Re: Problems Phylip

Joe Felsenstein via mol-evol%40net.bio.net (by joe from removethispart.gs.washington.edu)
Mon Oct 30 11:20:51 EST 2006


In article <mailman.259.1162214961.23274.mol-evol from net.bio.net>,
christ  <christophe.jestin from rennes.inra.fr> wrote:

>When i used Phylip to obtain the distance matrix, instead of a distance I
>obtained "1.#QNAN0", and so I can't do the program Neighbor because of
>"1.#QNAN0".
>Can you help me, please? Thank you in advance.  

NAN may mean "not a number".  It probably means that no distance can be
computed between those two sequences (I assume you are using DNA sequences
but you never said whether you were using Protdist, Dnadist, Gendist, or
Restdist).  One should look at those two sequences and see what they are.
If they have, say, lots of gaps and no bases in common there could be a
result like this.

I am a bit confused (aside from the issue of what program you are talking
about, and what the data look like) by the "1.#QNAN0"  The program should
not ever print that "1." in the output file.  Is this in the output file
or is it what appears on the screen?  If so it might be a species name
instead!

To the rest of you out there, this will give you a good idea of the
difficulty of doing user support when the user supplies only cryptic
information.

----
Joe Felsenstein         joe from removethispart.gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 357730, Seattle, WA 98195-7730 USA
AFTER DECEMBER 15, 2006 change that line to:
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA



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