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PHYLIP protdist units?

Brian Foley btf at t10.lanl.gov
Thu May 7 18:17:46 EST 1998

I have a nucleotide alignment, that I also translated into
protein.  Using dnadist to generate a distance matrix, I 
get values close to the % difference between sequence pairs
(i.e. if two sequences are 93% identical, the value I get
is close to 0.07).  However, when I run protdist, using the
categories model, I get values over 1.0 in some cases (for
sequences with % identity near 80%).

I was hoping that both protdist and dnadist values would be
close to % difference, but adjusted for different types of
mutations (i.e. in dnadist I can weight transisitons
lower than transversions and in protdist I can use different
substutution matrices to count an Ile -> Leu change as less
significant than an Ile -> Tyr change).

Are the distance units calculated by protdist using the
categories model meanigful in any concrete way?  Is there
a conversion program to convert from those values to something
more like % distance (i.e. values between 0 and 1)? 

|Brian T. Foley               btf at t10.lanl.gov                       |
|HIV Database                 (505) 665-1970                         |
|Los Alamos National Lab      http://hiv-web.lanl.gov/index.html     |
|Los Alamos, NM 87544  U.S.A. http://www.t10.lanl.gov/~btf/home.html |

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