Data for recombination/LD analysis, viruses

This is the raw source data and code used in this experiment. All necessary packages are imported in the code. Python 3.12 was used. Jupyter Notebooks were run using JupyterLab 4.3.4. (1) The FASTA file, ALIGNEDSEQ213.fasta, includes the 213 monkeypox/mpox (MPXV) Ib sequences used in this analysis. (2) The Python file, sequence_remover.py, removed sequences with >2,000 ambiguous bases to create the 213 MPXV Ib sequences. (3) The Excel file, HaploviewPrep.xlsx, shows the processing steps of the SNPs extracted from the MSA using CodonCode, to create the .ped and .txt files needed for the LINKAGE formatted input in Haploview. (4) The LD file, HAPLOVIEWLDFILE, contains the exported data from Haploview. (5) The Python file, pair_counter.py, contains the code that developed the haplotype frequencies for each RSP. sampleFile.xlsx contains a reformatted .ped file, while pairsFile.xlsx contains the SNP pairs predicted by Haploview. These two files are inputs for pair_counter.py. (6) The Jupyter Notebook files, Non_Closed_Equation_Calculator.ipynb and Parameter_Calculator.ipynb, were used to calculate AfH,max outputs for equation 21 and 27.