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Code for doing the simulations in the manuscript: "Disentangling genetic and epigenetic determinants of ultrafast adaptation" Gjuvsland et al submitted to Molecular Systems Biology

==== General Options ==================

-m mutations rate per genome per cell division

-s shape value for gamma distribution

-l scale value for gamma distribution

-f proportion of fitness affecting mutations

-b proportion of beneficial mutations in fitness affecting mutation

-L Include Lag or not. 0 means Lag is not included. 1 means Lag is included

-t Type of simulation "ee" for simulating adaptation across the realistic range of mutation parameter values, "ca" for competition assays, "mt" for simulating experimental evolution with mutations in FPS1, ASK10, ACR3

==== In-silico selection experiment: Only Rate part is included for in-silico selection experiment ==============

Initial population contains only wild type cells. New mutations will be introduced based on given mutation rate. Fitness values for mutations are based on given fitness parameters. Mutations can be deleterious or neutral or beneficial to cells' fitness.

Code example: python setup.py build_ext --inplace python Yeast_Simulator.py -m 0.004 -s 2 -l 33 -f 50 -b 50 -L 0 -t 0 #mutations affect rate only

==== Individual-based competition assays =========================

A single mutant is included with WT population and allowed to grow in stress environment, no new mutations are introduced. The mutant has an advantage over WT in the stress environment (modify values in Yeast_Simulator.py).

Code example: python setup.py build_ext --inplace python Yeast_Simulator.py -L 1 -t 1 #rate and lag

==== Simulating experimental evolution with mutations in FPS1, ASK10, ACR3 ===================

Lag and Rate part is included for in-silico selection experiment. Plus, mutation target size can be included. And, Fitness effect of mutations should be included.

Code example: python setup.py build_ext --inplace python Yeast_Simulator.py -m 0.004 -L 1 -t 2

Input file: Target names, size and fitness values. File name should be "Target.txt" e.g. FPS1 276 130 600 ASK10_5_P3 498 133 1300 ACR3_5_P2 611 123 1600

In row 1, FPS1 is the target gene name. 276 (minutes) is the time a cell takes in lag phase. 130 (minutes) is a cell takes in rate phase. 600 (base pairs) is the size of the target in Yeast genome. If the randomly selected mutation falls with this 600 basepairs, that call will spend 276 minutes in lag phase and 130 minutes in rate phase.