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
biopytools/admixture/config.py
biopytools/admixture/data_processing.py
biopytools/admixture/main.py
biopytools/admixture/results.py
biopytools/admixture/utils.py
biopytools/agp2table/__init__.py
biopytools/agp2table/config.py
biopytools/agp2table/main.py
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biopytools/aliner/__init__.py
biopytools/aliner/config.py
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biopytools/allhic/asmkit.py
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biopytools/annorefine/__init__.py
biopytools/annorefine/config.py
biopytools/annorefine/evidence.py
biopytools/annorefine/expression.py
biopytools/annorefine/gap_analysis.py
biopytools/annorefine/main.py
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biopytools/annorefine/model_build.py
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biopytools/annorefine/ssp.py
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biopytools/annovar/__init__.py
biopytools/annovar/annotation.py
biopytools/annovar/config.py
biopytools/annovar/data_processing.py
biopytools/annovar/main.py
biopytools/annovar/results.py
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biopytools/assembly2agp/__init__.py
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biopytools/assembly_qc/__init__.py
biopytools/assembly_qc/busco_evaluator.py
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biopytools/assembly_qc/long_read_mapping_evaluator.py
biopytools/assembly_qc/main.py
biopytools/assembly_qc/mapping_evaluator.py
biopytools/assembly_qc/qv_evaluator.py
biopytools/assembly_qc/report_generator.py
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biopytools/assembly_qv/__init__.py
biopytools/assembly_qv/config.py
biopytools/assembly_qv/main.py
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biopytools/assembly_stats/__init__.py
biopytools/assembly_stats/config.py
biopytools/assembly_stats/main.py
biopytools/assembly_stats/stats_analyzer.py
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biopytools/atomm/__init__.py
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biopytools/atomm/convert.py
biopytools/atomm/kinship.py
biopytools/atomm/main.py
biopytools/atomm/model.py
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biopytools/bam2fastq/__init__.py
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biopytools/bam_cov/__init__.py
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biopytools/bam_stats/config.py
biopytools/bam_stats/core.py
biopytools/bam_stats/coverage_stats.py
biopytools/bam_stats/duplicate_stats.py
biopytools/bam_stats/genome_stats.py
biopytools/bam_stats/insert_stats.py
biopytools/bam_stats/main.py
biopytools/bam_stats/sample_stats.py
biopytools/bam_stats/sequence_stats.py
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biopytools/bam_view/__init__.py
biopytools/bam_view/calculator.py
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biopytools/bismark/core_analysis.py
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biopytools/blast/__init__.py
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biopytools/blast/html_templates.py
biopytools/blast/main.py
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biopytools/blast/text_alignment.py
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biopytools/braker/__init__.py
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biopytools/braker/main.py
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biopytools/braker4phyto/__init__.py
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biopytools/busco/__init__.py
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biopytools/bwa/__init__.py
biopytools/bwa/alignment.py
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biopytools/bwa/coverage.py
biopytools/bwa/genome.py
biopytools/bwa/main.py
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biopytools/bwa_gatk/__init__.py
biopytools/bwa_gatk/alignment.py
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biopytools/bwa_gatk/filtering.py
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biopytools/bwa_gatk/sample_detector.py
biopytools/bwa_gatk/statistics.py
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biopytools/bwa_gatk/variant_calling.py
biopytools/cactus/__init__.py
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biopytools/cactus/config.py
biopytools/cactus/pangenome.py
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biopytools/cli/commands/genomesyn.py
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biopytools/cli/commands/indelpav.py
biopytools/cli/commands/insert2locus.py
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biopytools/cli/commands/iqtree.py
biopytools/cli/commands/iseq.py
biopytools/cli/commands/janusx.py
biopytools/cli/commands/jcvi.py
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biopytools/cli/commands/kraken2.py
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biopytools/cli/commands/longestmrna.py
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biopytools/cli/commands/mafft_fasttree.py
biopytools/cli/commands/mcyc.py
biopytools/cli/commands/meme_parser.py
biopytools/cli/commands/merge_deepbsa.py
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biopytools/cli/commands/microsynteny.py
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biopytools/cli/commands/needle_identity.py
biopytools/cli/commands/ngenomesyn.py
biopytools/cli/commands/nlr_annotator.py
biopytools/cli/commands/ocbsa.py
biopytools/cli/commands/oomycete_anno.py
biopytools/cli/commands/orthofinder.py
biopytools/cli/commands/pair_fastq.py
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biopytools/cli/commands/panedta.py
biopytools/cli/commands/panhite.py
biopytools/cli/commands/panman.py
biopytools/cli/commands/panvar.py
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biopytools/cli/commands/parse_seq.py
biopytools/cli/commands/pep2genome.py
biopytools/cli/commands/pggb.py
biopytools/cli/commands/phobius.py
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biopytools/cli/commands/phylo_trim.py
biopytools/cli/commands/phyto_effector.py
biopytools/cli/commands/pi.py
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biopytools/cli/commands/picrust2.py
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biopytools/cli/commands/rxlr_scanner.py
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biopytools/extract_reads/extractor.py
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biopytools/fastp/pair_fix_mixin.py
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biopytools/repeatmask/__init__.py
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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
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biopytools/rnaseq/main.py
biopytools/rnaseq/quantification.py
biopytools/rnaseq/results.py
biopytools/rnaseq/utils.py
biopytools/rnaseq2vcf/__init__.py
biopytools/rnaseq2vcf/config.py
biopytools/rnaseq2vcf/data_processing.py
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biopytools/rnaseq2vcf/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
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biopytools/rxlr_scanner/__init__.py
biopytools/rxlr_scanner/config.py
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biopytools/rxlr_scanner/scanner.py
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biopytools/samplot/__init__.py
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biopytools/samplot/main.py
biopytools/samplot/utils.py
biopytools/selective_sweep/__init__.py
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biopytools/selective_sweep/merge_stats.py
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biopytools/seq2genome/__init__.py
biopytools/seq2genome/calculator.py
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biopytools/seq2genome/gff3_exporter.py
biopytools/seq2genome/main.py
biopytools/seq2genome/parser.py
biopytools/seq2genome/sequence_extractor.py
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biopytools/seq_extract/__init__.py
biopytools/seq_extract/config.py
biopytools/seq_extract/main.py
biopytools/seq_extract/utils.py
biopytools/seq_len/__init__.py
biopytools/seq_len/calculator.py
biopytools/seq_len/config.py
biopytools/seq_len/main.py
biopytools/seq_len/utils.py
biopytools/signalp/__init__.py
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biopytools/smudgescope/__init__.py
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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
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biopytools/split_fasta_id/__init__.py
biopytools/split_fasta_id/config.py
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biopytools/split_fasta_id/processor.py
biopytools/split_fasta_id/utils.py
biopytools/sra2fastq/__init__.py
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biopytools/sra2fastq/main.py
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biopytools/sra2fastq/report.py
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biopytools/subgenome_assign/__init__.py
biopytools/subgenome_assign/aligner.py
biopytools/subgenome_assign/assigner.py
biopytools/subgenome_assign/config.py
biopytools/subgenome_assign/main.py
biopytools/subgenome_assign/splitter.py
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biopytools/subphase/__init__.py
biopytools/subphase/config.py
biopytools/subphase/main.py
biopytools/subphase/utils.py
biopytools/subseq/__init__.py
biopytools/subseq/core.py
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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
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biopytools/telocomp/__init__.py
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biopytools/tgsgapcloser/__init__.py
biopytools/tgsgapcloser/config.py
biopytools/tgsgapcloser/main.py
biopytools/tgsgapcloser/quartet_filler.py
biopytools/tgsgapcloser/utils.py
biopytools/tmhmm/__init__.py
biopytools/tmhmm/config.py
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biopytools/transcript_assembly/__init__.py
biopytools/transcript_assembly/assembly.py
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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
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biopytools/treemix/__init__.py
biopytools/treemix/cli.py
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biopytools/treemix/runner.py
biopytools/treemix/utils.py
biopytools/trimal/__init__.py
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biopytools/trimal/main.py
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biopytools/vcf2gene/__init__.py
biopytools/vcf2gene/calculator.py
biopytools/vcf2gene/config.py
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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
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biopytools/vcf2nj/distance_calc.py
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biopytools/vcf2nj/tree_builder.py
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biopytools/vcf2pav/__init__.py
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biopytools/vcf2pav/converter.py
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biopytools/vcf2pav/utils.py
biopytools/vcf2pca/__init__.py
biopytools/vcf2pca/config.py
biopytools/vcf2pca/data_processing.py
biopytools/vcf2pca/main.py
biopytools/vcf2pca/pca_analysis.py
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biopytools/vcf2pca/utils.py
biopytools/vcf2pca/v2p_analyzer.py
biopytools/vcf2pca/visualization.py
biopytools/vcf2phylip/__init__.py
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biopytools/vcf2phylip/main.py
biopytools/vcf2phylip/matrix_writer.py
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biopytools/vcf2tree/__init__.py
biopytools/vcf2tree/config.py
biopytools/vcf2tree/fasttree_builder.py
biopytools/vcf2tree/iqtree_builder.py
biopytools/vcf2tree/main.py
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biopytools/vcf2tree/vcf_converter.py
biopytools/vcf_filter/__init__.py
biopytools/vcf_filter/analyzer.py
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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
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biopytools/vcf_pca/__init__.py
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biopytools/vcf_pca/pca_analysis.py
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biopytools/vcf_renamer/__init__.py
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biopytools/vcf_sample_hete/__init__.py
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biopytools/vcf_sample_hete/data_processing.py
biopytools/vcf_sample_hete/main.py
biopytools/vcf_sample_hete/results.py
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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
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biopytools/wgdi/utils.py
biopytools/wgsim/__init__.py
biopytools/wgsim/config.py
biopytools/wgsim/main.py
biopytools/wgsim/utils.py
biopytools/xpclr/__init__.py
biopytools/xpclr/calculator.py
biopytools/xpclr/config.py
biopytools/xpclr/main.py
biopytools/xpclr/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/aliner.md
docs/allelic_genes.md
docs/allhic.md
docs/annorefine.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_cov.md
docs/bam_stats.md
docs/bam_view.md
docs/bismark.md
docs/blast.md
docs/braker.md
docs/braker4phyto.md
docs/busco.md
docs/bwa.md
docs/bwa_gatk.md
docs/cactus.md
docs/centier.md
docs/chr_rename.md
docs/cim.md
docs/conda_env_software_map.md
docs/coverage.md
docs/coverage_filter.md
docs/cphasing.md
docs/deepbsa.md
docs/deeploc.md
docs/deeptmhmm.md
docs/dsuite.md
docs/dual_rnaseq.md
docs/easyhap.md
docs/edta.md
docs/egapx_batch.md
docs/eggnog_mapper.md
docs/ena_downloader.md
docs/eviann.md
docs/extract_reads.md
docs/faprotaxtax.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/fof.md
docs/fst.md
docs/func_anno.md
docs/gap_fill.md
docs/gap_stat.md
docs/gatk_joint.md
docs/gctb.md
docs/gemma_gwas.md
docs/gene_density.md
docs/gene_rnaseq_check.md
docs/gene_table.md
docs/genebank2fasta.md
docs/geneinfo.md
docs/genome2sv.md
docs/genome2tree.md
docs/genome_mount_rate.md
docs/genomeasm.md
docs/genomesyn.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/gtf2gff.md
docs/gtx.md
docs/gtx_joint.md
docs/gwas2gene.md
docs/gwas_gec.md
docs/gwas_lambda.md
docs/hap_type.md
docs/haphic.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/indel_marker.md
docs/indelpav.md
docs/index.md
docs/insert2locus.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/kmeria.md
docs/kmertools.md
docs/kraken2.md
docs/lai.md
docs/ldblockshow.md
docs/longestmrna.md
docs/longrnaseq.md
docs/mafft_fasttree.md
docs/mcyc.md
docs/meme_parser.md
docs/mga.md
docs/microsynteny.md
docs/minibwa.md
docs/minigraph.md
docs/minimap2.md
docs/mixrace.md
docs/module_groups.md
docs/msa.md
docs/msaviz.md
docs/ncbi_taxo.md
docs/needle_identity.md
docs/ngenomesyn.md
docs/nlr_annotator.md
docs/ocbsa.md
docs/oomycete_anno.md
docs/orthofinder.md
docs/pair_fastq.md
docs/pan_blocks.md
docs/pandepth.md
docs/panedta.md
docs/panhite.md
docs/panman.md
docs/panvar.md
docs/parabricks.md
docs/parse_gene_dna.md
docs/parse_seq.md
docs/pep2genome.md
docs/pggb.md
docs/phobius.md
docs/phylo_selector.md
docs/phylo_trim.md
docs/phyto_effector.md
docs/pi.md
docs/pi4gene.md
docs/picrust2.md
docs/pixy.md
docs/plinkgwas.md
docs/plotsr.md
docs/poplddecay.md
docs/predgpi.md
docs/primer3.md
docs/promoter_extractor.md
docs/protein_stats.md
docs/psvcp.md
docs/purge_dups.md
docs/qiime2.md
docs/ragtag.md
docs/raxml.md
docs/raxml_ng.md
docs/rename_chromosomes.md
docs/rename_genome_id.md
docs/repeat_analyzer.md
docs/repeatmask.md
docs/resistify.md
docs/rmvp.md
docs/rnabloom.md
docs/rnaseq.md
docs/rnaseq2vcf.md
docs/rnaseq_val.md
docs/rxlr_scanner.md
docs/samplot.md
docs/selective_sweep.md
docs/seq2genome.md
docs/seq_extract.md
docs/seq_len.md
docs/signalp.md
docs/smudgescope.md
docs/snp_index.md
docs/snp_region_gene.md
docs/split_fasta_id.md
docs/sra2fastq.md
docs/subgenome_assign.md
docs/subphaser.md
docs/subseq.md
docs/swave.md
docs/tassel_gwas.md
docs/telocomp.md
docs/tmhmm.md
docs/transcript_assembly.md
docs/treemix.md
docs/trimal.md
docs/vcf2gene.md
docs/vcf2genotype.md
docs/vcf2gwas.md
docs/vcf2nj.md
docs/vcf2pav.md
docs/vcf2pca.md
docs/vcf2phylip.md
docs/vcf2tree.md
docs/vcf_filter.md
docs/vcf_merger.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/xpclr.md
docs/yahs.md
docs/dev-standards/01_module_template.md
docs/dev-standards/02_logging_detail.md
docs/dev-standards/11_path_management.md
docs/dev-standards/12_output_naming.md
docs/dev-standards/13_conda_invocation.md
docs/dev-standards/14_tool_invocation_policy.md
scripts/analyze_conda_envs_merge.py
scripts/analyze_env_name_fields.py
scripts/analyze_full_deletion.py
scripts/audit_conda_envs.py
scripts/check_docs.py
scripts/gen_docs_nav.py
scripts/gen_docs_params.py
scripts/gen_software_map.py