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R, python, and perl scripts used to analyze genomic data from Drosophila museum specimens

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Calculate_Fraction_Masked.R
Calculate_Fraction_Masked.R
 
 
Compare_WithinGenome_ChrX_Pi.R
Compare_WithinGenome_ChrX_Pi.R
 
 
Compare_WithinGenome_Population_Pi.R
Compare_WithinGenome_Population_Pi.R
 
 
Count_Singletons_AT.R
Count_Singletons_AT.R
 
 
Downsample_NoMasking_ForPCA.R
Downsample_NoMasking_ForPCA.R
 
 
Estimate_Genetic_Distance_NoNA.R
Estimate_Genetic_Distance_NoNA.R
 
 
Estimate_Pop_Size_Bayesian_NoIBD_SingleChr3L.R
Estimate_Pop_Size_Bayesian_NoIBD_SingleChr3L.R
 
 
Estimate_Pop_Size_Bayesian_NoIBD_SingleChr3L_1800.R
Estimate_Pop_Size_Bayesian_NoIBD_SingleChr3L_1800.R
 
 
File_Summary.txt
File_Summary.txt
 
 
GO_overlap_parallel.pl
GO_overlap_parallel.pl
 
 
Identify_IBD_Regions_Autosome_Final.R
Identify_IBD_Regions_Autosome_Final.R
 
 
Identify_IBD_Regions_ChrX_Final.R
Identify_IBD_Regions_ChrX_Final.R
 
 
In2Lt_fixeddiff_kapun.txt
In2Lt_fixeddiff_kapun.txt
 
 
In2RNs_fixeddiff_kapun.txt
In2RNs_fixeddiff_kapun.txt
 
 
In3LP_fixeddiff_kapun.txt
In3LP_fixeddiff_kapun.txt
 
 
In3RC_fixeddiff_kapun.txt
In3RC_fixeddiff_kapun.txt
 
 
In3RK_fixeddiff_kapun.txt
In3RK_fixeddiff_kapun.txt
 
 
In3RMo_fixeddiff_kapun.txt
In3RMo_fixeddiff_kapun.txt
 
 
In3RPayne_fixeddiff_kapun.txt
In3RPayne_fixeddiff_kapun.txt
 
 
Inversion_Recalc.R
Inversion_Recalc.R
 
 
Mask_Count_Homozygous_IBD_Regions.R
Mask_Count_Homozygous_IBD_Regions.R
 
 
Mask_Countfile_Windows.R
Mask_Countfile_Windows.R
 
 
Mask_Homozygous_IBD_Regions.R
Mask_Homozygous_IBD_Regions.R
 
 
PLOSBio_2023.tar.gz
PLOSBio_2023.tar.gz
 
 
README.md
README.md
 
 
calc_fst_from_ms_demog.py
calc_fst_from_ms_demog.py
 
 
call_haplotypes_var_only.py
call_haplotypes_var_only.py
 
 
effective_sample_size_short.py
effective_sample_size_short.py
 
 
effective_sample_size_short_haploidX.py
effective_sample_size_short_haploidX.py
 
 
freqshow_mixed_haploid_and_full_diploid.pl
freqshow_mixed_haploid_and_full_diploid.pl
 
 
make_site_depth_file.py
make_site_depth_file.py
 
 
outlier_regions.pl
outlier_regions.pl
 
 
pbe_from_counts_fst_corrected.pl
pbe_from_counts_fst_corrected.pl
 
 
remove_lowfreq_heterozygotes.py
remove_lowfreq_heterozygotes.py
 
 
simulate_history_ms_lundsplit_3L.py
simulate_history_ms_lundsplit_3L.py
 
 
windows_ZI25000_Chr2L.txt
windows_ZI25000_Chr2L.txt
 
 
windows_ZI25000_Chr2R.txt
windows_ZI25000_Chr2R.txt
 
 
windows_ZI25000_Chr3L.txt
windows_ZI25000_Chr3L.txt
 
 
windows_ZI25000_Chr3R.txt
windows_ZI25000_Chr3R.txt
 
 
windows_ZI25000_ChrX.txt
windows_ZI25000_ChrX.txt
 
 

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Museum_Drosophila_Genomes

R, python, and perl scripts used to analyze genomic data from Drosophila museum specimens

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R, python, and perl scripts used to analyze genomic data from Drosophila museum specimens

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