Substantial progress on the Perl model of USS evolution.
First the undergrad and I added the code that tallies up the scores of every sliding-window position in the genome. It didn't take us long to get it running (a few stray semicolons, etc.) However after now Keith's comment on yesterday's post I think there are more efficient ways to do what we've done.
Then we created code that does the recombination a completely different way, so each of the fragments being tested has its own chance to recombine (probability of recombination depends on its score). The code wasn't tricky, but getting it running took ages of tracking down stray curly brackets and discovering that I can't nest two 'while' loops (I changed one of them to an internal 'if' test).
I still need to add in the feature I came up with yesterday, that writes out the genome sequence and the tally of scores only at specified intervals, but now I have to dash off to a 'visioning education' meeting imposed on us by the administration.
The Green Sulphur Bacteria
3 hours ago in Catalogue of Organisms