Joined: June 2009
|Quote (Steve Schaffner @ June 11 2009,13:02)|
|For those who have the program running . . . Can it provide more output? Comparing results with theory would be much more straightforward if one could count only the number of mutations that have fixed, rather than all present in the population; it would also be useful to see the allele frequency spectrum. (And if it can't do those things, then it is of no interest as a population genetics tool.)|
Is the allele frequency spectrum you're looking for in here?
Box.net - human1 sample Folder
I think what you're looking for might be titled "human1_plm.png".
The output files in MENDEL do give a count for the number of fixed alleles; it's near the bottom of the output file and looks like this:
|Code Sample |
Allele summary statistics (tracked mutations only):
(Statistics are based on 891517 tracked deleterious mutations
and 0 tracked favorable mutations.)
Very rare Polymorphic Fixed Total
(0-1%) (1-99%) (100%)
15107 8202 0 23309 deleterious
0 0 0 0 favorable