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preprint doi:https://doi.org/10.1101/2024.10.02.614758

data folder: organised by Figure

Data points per generation:

• seqscommon : plastic genotypes abundance
• extreme0 : genotypes with only target 0
• extreme1: genotypes with only target 1
• other: rest of gentoypes, noise.
• meanfitness: mean fitness of the population
• meanprobs0: population mean of Boltzmann probability on target 0
• meanprobs1: population mean of Boltzmann probability on target 1

(ignore seqstarget, meanprobs0seqscom, meanprobs1seqscom, and alphalist)

• NDsetsize.pkl is the dictionary of secondary structures' NSS for the RNA12 ND GP map.

• pairs.csv is the mu (X) and delta t (Y) combinations for the parameter_sweep .py files to create the heatmaps

• phenopairs.pkl is an initial dictionary with targetpairs from which we select the pair 130 (key is 130) for the example in Fig.2.

• RNA12 ND GP map data such as folddict (keys are secondary structures and values are lists of sequences and Boltzmann probability corresponding to that structure) or dictRNA12tot (the full ND GP map) is inhttps://universityofcambridgecloud-my.sharepoint.com/:f:/r/personal/pg520_cam_ac_uk/Documents/NDgpmaps2022/Paper/RNA12/Datatot?csf=1&web=1&e=yzqaOi

• sequence.fasta: download fromhttps://dbarchive.biosciencedbc.jp/data/frnadb/LATEST/Sequence_Data/?C=D;O=A from sequence.zip or from link below

• selected_for_analysis: download fromhttps://universityofcambridgecloud-my.sharepoint.com/:f:/r/personal/pg520_cam_ac_uk/Documents/RNAplasticitydata?csf=1&web=1&e=s2CC20

-functions folder:

• evodyn001_* are .py files for Fig.2 example targetpair.
• evodyn_regimes_sweep_* are .py files dealing with the targetpairs from different categories. (cc, cs, ss) (0,1,2)
• cc is complex-complex (both small NSS), cs is complex-simple (mixed NSS) and simple-simple (large NSS).
• 0 is small, 1 is medium and 2 is large Hamming distance.

gmapfunctions, phenotypesearchfinal, and targetpairs and data_genotype_targetpairs deal with categorising targetpairs according to NSS and Hamming distance as well as producing their genotype populations

evodyn_seqs.ipynb is a notebook used to produce plots and test data.

functionalRNAplots.ipynb: produce plot for functional RNA.

-plots folder: .png files of plots