RAD_scripts

These are scripts for various tasks associated with analysing RADseq datasets.

Name		Name	Last commit message	Last commit date
Latest commit History 236 Commits
HyDe_input.py		HyDe_input.py
LICENSE		LICENSE
MM_ipyrad_summary.R		MM_ipyrad_summary.R
MY_replicate_error.R		MY_replicate_error.R
PCA_plot.R		PCA_plot.R
README.md		README.md
SNAPP_divergence.R		SNAPP_divergence.R
Tiger_error_plot.py		Tiger_error_plot.py
bestK_Evanno.py		bestK_Evanno.py
clone_report.py		clone_report.py
collate_clones.py		collate_clones.py
concord_to_newick.py		concord_to_newick.py
dartR_filter.rmd		dartR_filter.rmd
dartR_filter_nondart.R		dartR_filter_nondart.R
distances.R		distances.R
filter.sh		filter.sh
filter_plot.R		filter_plot.R
filter_vcf.py		filter_vcf.py
fst_heatmap.R		fst_heatmap.R
generate_seqs.py		generate_seqs.py
het_pca_plot.R		het_pca_plot.R
isolation_by_distance.R		isolation_by_distance.R
lea_tess.R		lea_tess.R
loci_extract.py		loci_extract.py
missing_plot.R		missing_plot.R
newhybrids_summary.py		newhybrids_summary.py
opt_ipyrad.sh		opt_ipyrad.sh
optim_snp_data.R		optim_snp_data.R
plot_tree.rmd		plot_tree.rmd
popgen_stats.R		popgen_stats.R
private_alleles.R		private_alleles.R
single_snp.py		single_snp.py
structure_barplots.py		structure_barplots.py
structure_summary_ipyrad.py		structure_summary_ipyrad.py
tetrad_summary.py		tetrad_summary.py
vcf_addPL.py		vcf_addPL.py
vcf_cover.R		vcf_cover.R
vcf_depth.py		vcf_depth.py
vcf_similarity.py		vcf_similarity.py
vcf_to_beagle.py		vcf_to_beagle.py
vcf_to_fasta.py		vcf_to_fasta.py
vcf_to_newhybs.py		vcf_to_newhybs.py
vcf_to_nexus.py		vcf_to_nexus.py
vcf_to_structure.py		vcf_to_structure.py
vcf_to_svd.py		vcf_to_svd.py

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