Welcome to Evolution simulation and classification project!

After measuring gene frequencies of modern populations that have a common ancestor, we estimate ancestral allele frequency and selection state for each gene. A bayesian model is used and verified using the included simulator.

Getting started

You can install the package and run a simulation using the following commands in R:

install.packages(c("animation","ggplot2")) # for dependencies on CRAN
install.packages("nicholsonppp", repos="http://R-Forge.R-project.org")
library(nicholsonppp)
sim <- sim.drift.selection()
df <- sim2df(sim)
## Plot 6 loci evolving over time:
loci.over.time(interesting.loci(df))
## Make an animation that summarizes the simulation:
evolution.animation(df)

Animations of allele frequency evolution simulation

Date Image size Generations 2009-08-10 1200x1000 200 2009-08-19 1000x800 200

Compiler notes

The package has been compiled successfully using gfortran and ifort. We prefer using ifort when possible, since it makes the program run faster. To use ifort with R you have to recompile R. Download the sources then do:

FC=ifort ./configure && make

Also make sure to add your ifort lib (something like intel/Compiler/11.0/081/lib/ia32) to the list of libraries (normally /etc/ld.so.conf), then run ldconfig. If you don't have root you may want to just set LD_LIBRARY_PATH to the ifort lib.

The project summary page you can find here.