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agat_convert_bed2gff.md
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agat_convert_embl2gff.md
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agat_convert_genscan2gff.md
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agat_convert_mfannot2gff.md
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agat_convert_minimap2_bam2gff.md
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agat_convert_sp_gff2bed.md
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agat_convert_sp_gff2gtf.md
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agat_convert_sp_gff2tsv.md
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agat_convert_sp_gff2zff.md
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agat_convert_sp_gxf2gxf.md
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agat_sp_Prokka_inferNameFromAttributes.md
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agat_sp_add_attribute_shortest_exon_size.md
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agat_sp_add_attribute_shortest_intron_size.md
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agat_sp_add_intergenic_regions.md
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agat_sp_add_introns.md
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agat_sp_add_splice_sites.md
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agat_sp_add_start_and_stop.md
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agat_sp_alignment_output_style.md
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agat_sp_clipN_seqExtremities_and_fixCoordinates.md
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agat_sp_compare_two_BUSCOs.md
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agat_sp_compare_two_annotations.md
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agat_sp_complement_annotations.md
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agat_sp_ensembl_output_style.md
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agat_sp_extract_attributes.md
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agat_sp_extract_sequences.md
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agat_sp_filter_by_ORF_size.md
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agat_sp_filter_by_locus_distance.md
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agat_sp_filter_by_mrnaBlastValue.md
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agat_sp_filter_feature_by_attribute_presence.md
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agat_sp_filter_feature_by_attribute_value.md
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agat_sp_filter_feature_from_keep_list.md
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agat_sp_filter_feature_from_kill_list.md
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agat_sp_filter_gene_by_intron_numbers.md
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agat_sp_filter_gene_by_length.md
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agat_sp_filter_incomplete_gene_coding_models.md
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agat_sp_filter_record_by_coordinates.md
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agat_sp_fix_cds_phases.md
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agat_sp_fix_features_locations_duplicated.md
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agat_sp_fix_fusion.md
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agat_sp_fix_longest_ORF.md
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agat_sp_fix_overlaping_genes.md
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agat_sp_fix_small_exon_from_extremities.md
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agat_sp_flag_premature_stop_codons.md
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agat_sp_flag_short_introns.md
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agat_sp_functional_statistics.md
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agat_sp_keep_longest_isoform.md
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agat_sp_kraken_assess_liftover.md
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agat_sp_list_short_introns.md
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agat_sp_load_function_from_protein_align.md
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agat_sp_manage_IDs.md
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agat_sp_manage_UTRs.md
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agat_sp_manage_attributes.md
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agat_sp_manage_functional_annotation.md
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agat_sp_manage_introns.md
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agat_sp_merge_annotations.md
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agat_sp_move_attributes_within_records.md
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agat_sp_prokka_fix_fragmented_gene_annotations.md
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agat_sp_sensitivity_specificity.md
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agat_sp_separate_by_record_type.md
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agat_sp_split_by_level2_feature.md
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agat_sp_statistics.md
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agat_sp_to_tabulated.md
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agat_sp_webApollo_compliant.md
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agat_sq_add_attributes_from_tsv.md
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agat_sq_add_hash_tag.md
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agat_sq_add_locus_tag.md
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agat_sq_count_attributes.md
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agat_sq_filter_feature_from_fasta.md
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agat_sq_list_attributes.md
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agat_sq_manage_IDs.md
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agat_sq_manage_attributes.md
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agat_sq_mask.md
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agat_sq_remove_redundant_entries.md
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agat_sq_repeats_analyzer.md
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agat_sq_reverse_complement.md
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agat_sq_rfam_analyzer.md
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agat_sq_split.md
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agat_sq_stat_basic.md
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