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Bneck sims

Using Tim's model

~~Do some bneck sims to show similarity and differences of bneck models.

See r code for descriptions of models.

SLIM sims

Doing some sims with SLIM to try look at deleterious variants and D.

Sims with fwdpp as well, in fwdpp.sh

Round 1

results files for first round of fwdpp sims in results, see bneck_ftw R code analysis for analysis details.~~

Files

split.pl takes ms output from fwdpp (which alternates netural/selected) and splits into two files. should automate rest of job to get msstats output

combine.pl takes ms output which alternates netural/selected and combines into one read block. No longer necessary as fwdpp code can write a combined ms block instead.

cleanup.sh takes ms output runs split.pl, msstats, writes to neutral and selected files for separate runs

bneck_selection_dist.cc is a modified version of the bneck_selection.cc code from Kevin Thornton's fwdpp. Instead of inputting a constant s on the command line, you enter the mean for an exponential and a percent of selected mutations which are positive. All selected mutations (positive and negative) are drawn from the same exponential.