LD_recomb

Code and data for:

Samuk, K., & Noor, M. A. F. (2022). Gene flow biases population genetic inference of recombination rate. G3 . https://doi.org/10.1093/g3journal/jkac236

Name		Name	Last commit message	Last commit date
bak		bak
data		data
figures		figures
functions		functions
manuscript		manuscript
meta		meta
pipeline		pipeline
readings		readings
scripts		scripts
slim_sim		slim_sim
vcf_test		vcf_test
.gitattributes		.gitattributes
.gitignore		.gitignore
01_run_sims_realistic_gene_flow.sh		01_run_sims_realistic_gene_flow.sh
01a_run_recomb_evolve_realistic_rates_gene_flow.R		01a_run_recomb_evolve_realistic_rates_gene_flow.R
01b_compute_fst.sh		01b_compute_fst.sh
02_make_lookup_tables.sh		02_make_lookup_tables.sh
03_choose_hyperparams.sh		03_choose_hyperparams.sh
04_create_sim_to_real_translation_table.R		04_create_sim_to_real_translation_table.R
05_downsample_and_optimize.sh		05_downsample_and_optimize.sh
06_run_inference_pipeline.sh		06_run_inference_pipeline.sh
07_pack_optimize_folder.sh		07_pack_optimize_folder.sh
08_launch_process_pyrho_script.sh		08_launch_process_pyrho_script.sh
09_process_pyrho_files.R		09_process_pyrho_files.R
10_summarize_pyrho_output.R		10_summarize_pyrho_output.R
11_figure2_figure3.R		11_figure2_figure3.R
12_figure4.R		12_figure4.R
13_figureS1.R		13_figureS1.R
14_statistical_tests.R		14_statistical_tests.R
LICENSE		LICENSE
README.md		README.md
recomb_pop_diff.Rproj		recomb_pop_diff.Rproj

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