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 |
|____________________________________________________________________|
