├── .DS_Store ├── README.md ├── README_compile.py ├── README_header.md ├── bwa_distance_filter.py ├── create_gowinda_file.py ├── csv_mean.py ├── dartcsv2vcf.py ├── fasta_exclude.py ├── fasta_include.py ├── fastq_barcodes2samplenames.py ├── fastq_bin_paired_reads.py ├── fastq_seqcount.py ├── gdmatrix2tree.py ├── goterms_from_uniprot_blast.py ├── input_examples ├── assignment_file.csv ├── blastn_file.txt ├── compare_file.csv ├── exclusion_file.txt ├── extraparams ├── factor_file.txt ├── fasta_file.fa ├── fst_file.txt ├── inclusion_file.txt ├── loci_file.txt ├── locusnames_file.txt ├── mainparams ├── markernumbers_file.txt ├── matrix_file.txt ├── order_file.txt ├── paramfile ├── pop_file.txt ├── pyrad_file.loci ├── sam_file.sam ├── samplenames_file.txt ├── snps_file.txt └── vcf_file.vcf ├── ipyrad_include.py ├── itertools_combinations.py ├── mapping_get_blastn_matches.py ├── mapping_get_bwa_matches.py ├── mapping_identify_blast_matches.py ├── nexus_append_label_groups.py ├── nexus_set_label_colors.py ├── popfile_from_clusters.py ├── popfile_from_vcf.py ├── popfile_match_vcf.py ├── popfile_randomize.py ├── popfile_toggleassign.py ├── pyrad2concat_fasta.py ├── pyrad2fasta.py ├── pyrad2migrate.py ├── pyrad_filter.py ├── pyrad_find_caps_markers.py ├── pyrad_include.py ├── pyrad_shared_loci.py ├── pyrad_trim.py ├── pyradclust2fasta.py ├── structure_mp.py ├── structure_mp_plot.py ├── to_be_cleaned_up ├── create_GO_file.py ├── gdmatrix2heatmap.py ├── mapping_get_bwa_matches_stringent.py ├── matching_consensus_loci.py ├── matching_loci_same_mapping.py ├── pyradloci2fasta_longest.py ├── pyradloci2fasta_specific_samples.py ├── pyradloci2fasta_specific_samples_alt.py ├── vcf2outflank.py ├── vcf_allele_freqs.py └── vcf_genotype_matrix.py ├── vcf2hapmatrix.py ├── vcf2introgress.py ├── vcf2tess.py ├── vcf_afd_filter.py ├── vcf_ancestry_matrix.py ├── vcf_append_simulated_crosses.py ├── vcf_clone_detect.py ├── vcf_contrast_samples.py ├── vcf_find_clones.py ├── vcf_gdmatrix.py ├── vcf_genotype_freqs.py ├── vcf_get_chrom_pos_from_number.py ├── vcf_include_chrom.py ├── vcf_minrep_filter.py ├── vcf_minrep_filter_abs.py ├── vcf_missing_data.py ├── vcf_pos_count.py ├── vcf_ragoo_order.py ├── vcf_read_trim.py ├── vcf_reference_loci.py ├── vcf_remap.py ├── vcf_remap2genome.py ├── vcf_remove_chrom.py ├── vcf_rename_loci.py ├── vcf_rename_samples.py ├── vcf_single_snp.py ├── vcf_spider.py └── vcf_splitfst.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pimbongaerts/radseq/HEAD/.DS_Store -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pimbongaerts/radseq/HEAD/README.md -------------------------------------------------------------------------------- /README_compile.py: 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