LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
biopytools/__init__.py
biopytools/_version.py
biopytools.egg-info/PKG-INFO
biopytools.egg-info/SOURCES.txt
biopytools.egg-info/dependency_links.txt
biopytools.egg-info/entry_points.txt
biopytools.egg-info/requires.txt
biopytools.egg-info/top_level.txt
biopytools/admixture/__init__.py
biopytools/admixture/analysis.py
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biopytools/admixture/data_processing.py
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biopytools/repeatmask/config.py
biopytools/repeatmask/core.py
biopytools/repeatmask/main.py
biopytools/repeatmask/utils.py
biopytools/resistify/__init__.py
biopytools/resistify/config.py
biopytools/resistify/main.py
biopytools/resistify/parser.py
biopytools/resistify/sequence_extractor.py
biopytools/resistify/utils.py
biopytools/resistify_parser/__init__.py
biopytools/resistify_parser/config.py
biopytools/resistify_parser/main.py
biopytools/resistify_parser/parser.py
biopytools/resistify_parser/sequence_extractor.py
biopytools/resistify_parser/utils.py
biopytools/rmvp/__init__.py
biopytools/rmvp/analyzer.py
biopytools/rmvp/cli.py
biopytools/rmvp/config.py
biopytools/rmvp/result_parser.py
biopytools/rmvp/rscript_generator.py
biopytools/rmvp/utils.py
biopytools/rnabloom/__init__.py
biopytools/rnabloom/assembler.py
biopytools/rnabloom/config.py
biopytools/rnabloom/main.py
biopytools/rnabloom/utils.py
biopytools/rnaseq/__init__.py
biopytools/rnaseq/alignment.py
biopytools/rnaseq/config.py
biopytools/rnaseq/data_processing.py
biopytools/rnaseq/main.py
biopytools/rnaseq/quantification.py
biopytools/rnaseq/results.py
biopytools/rnaseq/utils.py
biopytools/rnaseq_val/__init__.py
biopytools/rnaseq_val/align_2nd.py
biopytools/rnaseq_val/align_3rd.py
biopytools/rnaseq_val/assemble_2nd.py
biopytools/rnaseq_val/assemble_3rd.py
biopytools/rnaseq_val/compare.py
biopytools/rnaseq_val/config.py
biopytools/rnaseq_val/correct.py
biopytools/rnaseq_val/main.py
biopytools/rnaseq_val/report.py
biopytools/rnaseq_val/utils.py
biopytools/rxlr_scanner/__init__.py
biopytools/rxlr_scanner/config.py
biopytools/rxlr_scanner/main.py
biopytools/rxlr_scanner/scanner.py
biopytools/rxlr_scanner/utils.py
biopytools/samplot/__init__.py
biopytools/samplot/config.py
biopytools/samplot/main.py
biopytools/samplot/utils.py
biopytools/seq2genome/__init__.py
biopytools/seq2genome/calculator.py
biopytools/seq2genome/config.py
biopytools/seq2genome/gff3_exporter.py
biopytools/seq2genome/main.py
biopytools/seq2genome/parser.py
biopytools/seq2genome/sequence_extractor.py
biopytools/seq2genome/statistics.py
biopytools/seq2genome/utils.py
biopytools/signalp/__init__.py
biopytools/signalp/config.py
biopytools/signalp/main.py
biopytools/signalp/utils.py
biopytools/smudgescope/__init__.py
biopytools/smudgescope/config.py
biopytools/smudgescope/main.py
biopytools/smudgescope/utils.py
biopytools/snp_index/__init__.py
biopytools/snp_index/analyzer.py
biopytools/snp_index/calculator.py
biopytools/snp_index/config.py
biopytools/snp_index/main.py
biopytools/snp_index/sliding_window.py
biopytools/snp_index/utils.py
biopytools/snp_index/visualizer.py
biopytools/snp_region_gene/__init__.py
biopytools/snp_region_gene/config.py
biopytools/snp_region_gene/main.py
biopytools/snp_region_gene/processor.py
biopytools/snp_region_gene/utils.py
biopytools/split_fasta_id/__init__.py
biopytools/split_fasta_id/config.py
biopytools/split_fasta_id/main.py
biopytools/split_fasta_id/processor.py
biopytools/split_fasta_id/utils.py
biopytools/sra2fastq/__init__.py
biopytools/sra2fastq/config.py
biopytools/sra2fastq/main.py
biopytools/sra2fastq/processor.py
biopytools/sra2fastq/report.py
biopytools/sra2fastq/utils.py
biopytools/subphase/__init__.py
biopytools/subphase/config.py
biopytools/subphase/main.py
biopytools/subphase/utils.py
biopytools/subseq/__init__.py
biopytools/subseq/core.py
biopytools/subseq/main.py
biopytools/subseq/simple_test.py
biopytools/subseq/test_example.py
biopytools/subseq/utils.py
biopytools/swave/__init__.py
biopytools/swave/config.py
biopytools/swave/main.py
biopytools/swave/pav_extractor.py
biopytools/swave/sv_caller.py
biopytools/swave/utils.py
biopytools/tassel_gwas/__init__.py
biopytools/tassel_gwas/batch_processor.py
biopytools/tassel_gwas/core.py
biopytools/tassel_gwas/main.py
biopytools/tassel_gwas/test_new_logic.py
biopytools/tassel_gwas/test_trait_detection.py
biopytools/tassel_gwas/utils.py
biopytools/telocomp/__init__.py
biopytools/telocomp/config.py
biopytools/telocomp/main.py
biopytools/telocomp/utils.py
biopytools/tmhmm/__init__.py
biopytools/tmhmm/config.py
biopytools/tmhmm/main.py
biopytools/tmhmm/utils.py
biopytools/transcript_assembly/__init__.py
biopytools/transcript_assembly/assembly.py
biopytools/transcript_assembly/config.py
biopytools/transcript_assembly/main.py
biopytools/transcript_assembly/utils.py
biopytools/transcriptome_prediction/__init__.py
biopytools/transcriptome_prediction/alignment.py
biopytools/transcriptome_prediction/annotation.py
biopytools/transcriptome_prediction/assembly.py
biopytools/transcriptome_prediction/coding_prediction.py
biopytools/transcriptome_prediction/config.py
biopytools/transcriptome_prediction/main.py
biopytools/transcriptome_prediction/utils.py
biopytools/treemix/__init__.py
biopytools/treemix/cli.py
biopytools/treemix/config.py
biopytools/treemix/runner.py
biopytools/treemix/utils.py
biopytools/vcf2gene/__init__.py
biopytools/vcf2gene/calculator.py
biopytools/vcf2gene/config.py
biopytools/vcf2gene/main.py
biopytools/vcf2gene/utils.py
biopytools/vcf2genotype/__init__.py
biopytools/vcf2genotype/config.py
biopytools/vcf2genotype/genotype_processor.py
biopytools/vcf2genotype/main.py
biopytools/vcf2genotype/output_formatter.py
biopytools/vcf2genotype/utils.py
biopytools/vcf2genotype/vcf_parser.py
biopytools/vcf2nj/__init__.py
biopytools/vcf2nj/config.py
biopytools/vcf2nj/distance_calc.py
biopytools/vcf2nj/main.py
biopytools/vcf2nj/results.py
biopytools/vcf2nj/tree_builder.py
biopytools/vcf2nj/utils.py
biopytools/vcf2pca/__init__.py
biopytools/vcf2pca/config.py
biopytools/vcf2pca/data_processing.py
biopytools/vcf2pca/main.py
biopytools/vcf2pca/pca_analysis.py
biopytools/vcf2pca/results.py
biopytools/vcf2pca/utils.py
biopytools/vcf2pca/v2p_analyzer.py
biopytools/vcf2pca/visualization.py
biopytools/vcf2phylip/__init__.py
biopytools/vcf2phylip/config.py
biopytools/vcf2phylip/main.py
biopytools/vcf2phylip/matrix_writer.py
biopytools/vcf2phylip/processor.py
biopytools/vcf2phylip/utils.py
biopytools/vcf2phylip/vcf_parser.py
biopytools/vcf_filter/__init__.py
biopytools/vcf_filter/analyzer.py
biopytools/vcf_filter/config.py
biopytools/vcf_filter/core.py
biopytools/vcf_filter/main.py
biopytools/vcf_filter/plink_converter.py
biopytools/vcf_filter/position_filter.py
biopytools/vcf_filter/python_filter.py
biopytools/vcf_filter/quality_filter.py
biopytools/vcf_filter/sample_filter.py
biopytools/vcf_filter/utils.py
biopytools/vcf_filter/variant_filter.py
biopytools/vcf_filter/vcf_reader.py
biopytools/vcf_merger/__init__.py
biopytools/vcf_merger/config.py
biopytools/vcf_merger/main.py
biopytools/vcf_merger/utils.py
biopytools/vcf_pca/__init__.py
biopytools/vcf_pca/config.py
biopytools/vcf_pca/data_processing.py
biopytools/vcf_pca/main.py
biopytools/vcf_pca/pca_analysis.py
biopytools/vcf_pca/results.py
biopytools/vcf_pca/utils.py
biopytools/vcf_pca/visualization.py
biopytools/vcf_renamer/__init__.py
biopytools/vcf_renamer/config.py
biopytools/vcf_renamer/main.py
biopytools/vcf_renamer/utils.py
biopytools/vcf_sample_hete/__init__.py
biopytools/vcf_sample_hete/config.py
biopytools/vcf_sample_hete/data_processing.py
biopytools/vcf_sample_hete/main.py
biopytools/vcf_sample_hete/results.py
biopytools/vcf_sample_hete/utils.py
biopytools/vcf_sampler/__init__.py
biopytools/vcf_sampler/config.py
biopytools/vcf_sampler/main.py
biopytools/vcf_sampler/sampler.py
biopytools/vcf_sampler/utils.py
biopytools/vcf_sequence/__init__.py
biopytools/vcf_sequence/config.py
biopytools/vcf_sequence/data_processing.py
biopytools/vcf_sequence/main.py
biopytools/vcf_sequence/results.py
biopytools/vcf_sequence/utils.py
biopytools/vg/__init__.py
biopytools/vg/config.py
biopytools/vg/construct.py
biopytools/vg/deconstruct.py
biopytools/vg/giraffe.py
biopytools/vg/index.py
biopytools/vg/main.py
biopytools/vg/utils.py
biopytools/wgdi/__init__.py
biopytools/wgdi/config.py
biopytools/wgdi/main.py
biopytools/wgdi/processor.py
biopytools/wgdi/utils.py
biopytools/wgsim/__init__.py
biopytools/wgsim/config.py
biopytools/wgsim/main.py
biopytools/wgsim/utils.py
biopytools/yahs/__init__.py
biopytools/yahs/config.py
biopytools/yahs/main.py
biopytools/yahs/pipeline.py
biopytools/yahs/steps.py
biopytools/yahs/utils.py
docs/admixture.md
docs/agp2table.md
docs/agp_converter.md
docs/allhic.md
docs/annovar.md
docs/assembly2agp.md
docs/assembly_qc.md
docs/assembly_qv.md
docs/assembly_stats.md
docs/atomm.md
docs/bam2fastq.md
docs/bam_coverage_stats.md
docs/bam_stats.md
docs/bam_view.md
docs/bismark.md
docs/blast.md
docs/blast_v2.md
docs/braker.md
docs/busco.md
docs/bwa.md
docs/cactus.md
docs/centier.md
docs/chr_rename.md
docs/chr_renamer.md
docs/cim.md
docs/coverage_filter.md
docs/cphasing.md
docs/deepbsa.md
docs/deeploc.md
docs/dsuit.md
docs/dsuite.md
docs/dual_rnaseq.md
docs/edta.md
docs/egapx-batch.md
docs/egapx_batch.md
docs/ena_downloader.md
docs/eviann.md
docs/extract_reads.md
docs/fastp.md
docs/fastq2vcf_gtx.md
docs/fastq2vcf_parabricks.md
docs/fastq_gc_filter.md
docs/fastq_stats.md
docs/filter_snp_indel.md
docs/find_telomere.md
docs/fst.md
docs/gap_fill.md
docs/gapstat.md
docs/gatk_joint.md
docs/gctb.md
docs/gemma-gwas.md
docs/genebank2fasta.md
docs/genome_mount_rate.md
docs/genomeasm.md
docs/genomescope.md
docs/genomesyn2.md
docs/get_link_from_CNCB.md
docs/get_plastome.md
docs/gff_renamer.md
docs/gffcompare.md
docs/gffconverter.md
docs/github_actions_release.md
docs/gtf2gff.md
docs/gtf_to_gff.md
docs/gtx-joint.md
docs/gtx_joint.md
docs/gwas-split-vcf.md
docs/gwas2gene.md
docs/gwas_gec.md
docs/gwas_lambda.md
docs/hap_type.md
docs/haphic.md
docs/haphic_changelog.md
docs/hic_heatmap.md
docs/hic_qc.md
docs/hicanu.md
docs/hifi_hic.md
docs/hifi_hic_workflow.md
docs/hifiasm.md
docs/hite.md
docs/hmmsearch.md
docs/indelpav.md
docs/insert_detection.md
docs/interproscan.md
docs/iqtree.md
docs/iseq.md
docs/janusx.md
docs/jcvi.md
docs/kaks.md
docs/kmc.md
docs/kmer2vcf.md
docs/kmeria.md
docs/kmeria_bin_viewer.md
docs/kmeria_input_format.md
docs/kmertools.md
docs/kmertools_compare.md
docs/kraken2.md
docs/lai.md
docs/ldblockshow.md
docs/longest_mrna.md
docs/longrnaseq.md
docs/mafft_fasttree.md
docs/mcyc.md
docs/meme_parser.md
docs/merge_deepbsa.md
docs/microsynteny.md
docs/minigraph.md
docs/minimap2.md
docs/msaviz.md
docs/ncbi_taxo.md
docs/ngenomesyn.md
docs/ngenomesyn_pipeline.md
docs/nlr_annotator.md
docs/ocbsa.md
docs/orthofinder.md
docs/pair_fastq.md
docs/pan_blocks.md
docs/pandepth.md
docs/panman.md
docs/panvar.md
docs/parabricks.md
docs/parse_gene_dna.md
docs/parse_gene_info.md
docs/parse_longest_mrna.md
docs/parse_sequence_vcf.md
docs/pep2genome.md
docs/pggb.md
docs/phylo_selector.md
docs/phyto_effector.md
docs/pi4gene.md
docs/picrust2.md
docs/pixy.md
docs/plink_fst.md
docs/plinkgwas.md
docs/plotsr.md
docs/poplddecay.md
docs/primer3.md
docs/promoter_extractor.md
docs/protein_stats.md
docs/purge_dups.md
docs/ragtag.md
docs/raxml.md
docs/rename_chromosomes.md
docs/rename_genome_id.md
docs/repeat_analyzer.md
docs/repeatmask.md
docs/resistify_parser.md
docs/rmvp.md
docs/rnabloom.md
docs/rnaseq.md
docs/run_genome_collinearity.md
docs/run_kmer_count.md
docs/run_kmer_extractor.md
docs/run_kmer_universal.md
docs/rxlr_scanner.md
docs/samplot.md
docs/seq2genome.md
docs/signalp.md
docs/smudgeplot.md
docs/smudgescope.md
docs/snp_index.md
docs/snp_region_gene.md
docs/split_fasta_id.md
docs/sra2fastq.md
docs/subphaser.md
docs/subseq.md
docs/subseq_examples.md
docs/sv_diversity.md
docs/swave.md
docs/tassel_gwas.md
docs/telocomp.md
docs/tgsgapcloser.md
docs/tmhmm.md
docs/transcript_assembly.md
docs/treemix.md
docs/vcf-renamer.md
docs/vcf2gene.md
docs/vcf2genotype.md
docs/vcf2gwas.md
docs/vcf2nj.md
docs/vcf2pca.md
docs/vcf2phylip.md
docs/vcf_filter.md
docs/vcf_merger.md
docs/vcf_pca.md
docs/vcf_phylo.md
docs/vcf_renamer.md
docs/vcf_sample_hete.md
docs/vcf_sampler.md
docs/vcf_sequence.md
docs/vg.md
docs/wgdi.md
docs/wgsim.md
docs/yahs.md