csv_files

A folder containing all of the csv files used to create the figures and perform statistical analyses

figures_statistics

Python script to create the figures and perform statistical analyses

sub_files

A folder containing all of the submission scripts for the Avida experiments. These files contain the parameters altered from the main Avida configuration file

create_csv_files

A folder containing all of the Python scripts to create csv files from Avida output

config_files

A folder containing all of the Avida configuration files

Two-loci two-allele model.

<p>The left panel shows the fitness landscapes and epistasis given by <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005960#pgen.1005960.e013" target="_blank">Eq (9)</a> in the first and second half of the simulation (updates 0–499: <i>w</i>₀ = 1 and <i>w</i>₁ = <i>w</i>₂ = <i>w</i>₃ = 10⁻⁵ ≈ 0; updates 500–1000: <i>w</i>₀ = <i>w</i>₃ = 1 and <i>w</i>₁ = <i>w</i>₂ = 10⁻⁵ ≈ 0). The xy-plane shows the four genotypes while the z-axis shows genotype fitness. The middle panel shows the genotype probabilities while the right panel shows the mutual information during the course of the simulation. Note that the increase in epistasis at the 500th update is reflected in the increase in mutual information. The mutation rate was 0.1 and starting population frequencies were <i>p</i>₀ = 1 and <i>p</i>₁ = <i>p</i>₂ = <i>p</i>₃ = 0.</p

Estimates of the information content of the HIV-1 protease.

<p>Filled black circles represent data from untreated subjects and blue triangles represent data from treated individuals. <i>I</i>₁ [see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005960#pgen.1005960.e017" target="_blank">Eq (12)</a>] is consistently low in treated sequence data over the years, indicating high sequence variability in the drug environment (top panel). The middle panel shows that the sum of pairwise mutual information significantly increases upon treatment (<i>p</i> ≤ 0.001). On adding the sum of pairwise mutual information to <i>I</i>₁, we obtain a comprehensive measure of information that considers pairwise interactions between residues [<i>I</i>₂, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005960#pgen.1005960.e018" target="_blank">Eq (13)</a>]. <i>I</i>₂ for both the treated and untreated data is comparable and unchanging over the years. We use data only for positions 15–90, as residues 1–14 as well as 91–99 have missing sequence data leading to error-prone estimates of entropy, as evidenced in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005960#pgen.1005960.s002" target="_blank">S2 Fig</a>. Error bars represent ±1 SD.</p

https://github.com/jacobclifford/MIBBS

MIBBS, Mutual Information Between Binding Sites, is a set of programs that generate all the figures for our Physical Biology paper, where the current program settings and input data are the same values as used in our Physical Biology paper. The git project contains a configure script to automatically compile our C/C++ code regardless of platform (see the README file in the MIBBS directory on github). Once one executes the configure script and runs make, then run masterscript.sh, which will create all eps files for all figures (see the README for necessary dependency programs, such as GNU Scientific Library and matlab (matlab is not necessary if one wishes to generate figures using some other utility))

dr_model

A Mathematica notebook that solves the drift robustness mathematical model

Final number of evolved phenotypic traits as a function of population size.

<p>Red lines are the median values for each population size. The upper and lower limits of each box denote the third and first quartile, respectively. Whiskers are 1.5 times the relevant quartile value. Plus signs denote those data points beyond the whiskers. Data represent only those populations that did not go extinct.</p