Method List
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#add_attribs Feature
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#add_child Feature
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#add_contig Dataset
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#add_feature Gff_dataset
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#add_go Contig
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#add_hit Contig
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#add_hsp Hit
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#add_localization Contig
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#add_master_feature Gff_dataset
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#add_parent_to Gff_dataset
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#add_snp Contig
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#add_uni_hsp Rebuild
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#align_contigs Dataset
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#align_len Hsp
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#array_contigs_to_contig Rebuild
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#attrib Feature
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#attrib_recover Dataset
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#attribs Feature
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#beg GO
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#build_gene_array Rebuild
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#cds Feature
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#change_to_type_id_recursive Feature
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#child Feature
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#clear_clusters Dataset
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#clr_contigs Dataset
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#cluster_count Dataset
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#cluster_filter Top Level Namespace
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#clustering Dataset
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#clusters Dataset
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#clusters_empty? Dataset
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#code GO
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#compare Hsp
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#compare Feature
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#compare Contig
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#compare_q Hsp
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#completed Contig
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#contig_compact Rebuild
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#contig_count Dataset
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#contigs Dataset
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#contigs_seq_merge Rebuild
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#convert_parsed_lines ExonerateResult
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#coor_intrones Contig
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#coord_prot Top Level Namespace
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#correct_hsp_contigs Dataset
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#correct_hsps Hit
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#correct_hsps Contig
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#correct_left_side_contigs Dataset
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#correct_model Rebuild
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#count Feature
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#create ReportGff
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#create Report
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#create_dataset Parser
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#dataset Gff_parser
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#dataset Parser
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#delete_cluster Dataset
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#delete_cluster_at Dataset
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#depth SNP
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#description Hit
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#draw Contig
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#drop_hsp Hit
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#e_value Hit
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#each_child Feature
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#each_cluster Dataset
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#each_cluster_with_index Dataset
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#each_contig Dataset
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#each_contig_with_index Dataset
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#each_feature Gff_dataset
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#each_go Contig
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#each_hit Contig
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#each_hit_with_index Contig
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#each_hsp Hit
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#each_id_feat Gff_dataset
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#each_id_master Gff_dataset
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#each_localization Contig
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#each_master_feature Gff_dataset
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#each_q_frameshift Contig
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#each_snp Contig
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#each_snp_with_index Contig
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#each_stop Contig
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#each_stop_with_index Contig
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#each_tag_attrib Feature
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#empty? ExonerateResult
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#end GO
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#eval_model Rebuild
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#exon_acumulative Contig
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#exones_q Contig
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#exones_s Contig
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#fasta Dataset
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#fasta_hash Top Level Namespace
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#feature Gff_dataset
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#filtering Dataset
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#filtering_clust Dataset
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#find_query ExonerateResult
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#first_hit Contig
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#first_hsp Hit
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#format_model Rebuild
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#gaps Hsp
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#gene_array_and_compact Rebuild
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#gene_array_report Rebuild
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#gene_compact Rebuild
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#gene_error Rebuild
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#gene_model_cut Rebuild
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#gene_stadistics Rebuild
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#gene_stadistics_report Rebuild
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#generate_file_5_prime Dataset
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#get Gff_dataset
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#gff Contig
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#gff_prot Contig
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#has_hit? Contig
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#has_source? Gff_dataset
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#has_type? Gff_dataset
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#hit_count Contig
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#hiting ExonerateResult
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#hits Contig
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#hits_sort! Contig
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#hsp_at Hit
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#hsp_at Contig
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#hsp_count Hit
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#hsp_minor_than? Contig
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#hsp_minor_than? Hit
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#hsp_overlap Hit
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#hsps Hit
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#hsps_sort! Hit
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#html_footer Top Level Namespace
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#html_header Top Level Namespace
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#html_link Top Level Namespace
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#html_row Top Level Namespace
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#html_table_footer Top Level Namespace
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#html_table_header Top Level Namespace
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#ident Hsp
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#index Gff_dataset
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#indices Contig
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#info_clusters Dataset
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#initialize ExonerateResult
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#initialize Gff_dataset
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#initialize Contig
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#initialize Gff_parser
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#initialize SNP
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#initialize BlastTypeParser
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#initialize Rebuild
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#initialize Hsp
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#initialize ExoBlastQuery
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#initialize Hit
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#initialize Feature
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#initialize GO
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#initialize Dataset
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#initialize Report
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#initialize Parser
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#inspect ExonerateResult
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#inspects Feature
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#inspects Gff_dataset
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#intrones_q Contig
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#is_gapped? Contig
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#is_one_hsp? Contig
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#is_source? Feature
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#is_truncated? Contig
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#is_type? Feature
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#last_hit Contig
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#last_hsp Hit
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#length Contig
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#length Feature
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#length2D Top Level Namespace
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#length_q Hsp
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#load_dataset BlastTypeParser
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#load_dataset Parser
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#load_references Dataset
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#load_seq Dataset
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#mapping Top Level Namespace
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#mapping_qual SNP
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#master_features Gff_dataset
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#missing_cluster_transfer Dataset
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#missing_contigs_transfer Dataset
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#mixed? Contig
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#mod_coord Contig
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#modeling_gene Rebuild
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#modified_coordenates Contig
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#multiple_align_contigs Dataset
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#n_contigs? Dataset
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#n_hits? Contig
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#n_intron Contig
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#name Contig
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#name GO
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#name Hit
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#obsolete GO
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#ontology GO
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#overlap Contig
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#overlap_test Rebuild
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#overlap_with Hsp
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#overlap_with Hit
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#parse_attribs Gff_parser
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#parse_contig_index Top Level Namespace
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#parse_file ParserBlast
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#parse_file Parser
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#parse_file ExonerateResult
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#parse_file ParserExonerate
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#parse_stops Dataset
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#phase Feature
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#populate_extra_atributes BlastTypeParser
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#populate_extra_atributes ParserExonerate
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#position SNP
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#position_reference_guided Rebuild
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#q_beg Hsp
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#q_end Hsp
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#q_frameshift ExoBlastQuery
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#q_frameshift Contig
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#q_p_conserved Hit
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#q_p_ident Hit
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#querys ExonerateResult
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#rebuild Rebuild
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#recover_test Rebuild
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#ref SNP
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#references_hash Dataset
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#report GffHsp
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#report GffHit
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#report GffFrameshift
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#report GffGo
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#report GffSNP
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#report Localization
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#report GffStop
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#report GffContig
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#rev Hsp
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#rev_comp Dataset
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#rev_comp Contig
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#rev_comp_if_hit Contig
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#rev_coord Contig
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#rev_coord Hsp
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#rev_coord Hit
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#reversed Hit
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#s_beg Hsp
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#s_end Hsp
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#s_frameshift Contig
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#s_frameshift ExoBlastQuery
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#s_length Hit
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#score Hsp
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#score Feature
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#score_correction Dataset
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#seq Contig
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#sides_add Top Level Namespace
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#sides_recovery Top Level Namespace
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#size ExonerateResult
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#sort_cluster Dataset
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#sort_cont_clust Dataset
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#source SNP
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#source Hit
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#source GO
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#source Feature
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#start Feature
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#start_codon_search Contig
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#stop Feature
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#stop_codon Contig
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#stop_codon_search Contig
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#stop_modified_coordenates Contig
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#stops Contig
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#strand Feature
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#strand_bias SNP
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#transfer_child Feature
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#transfer_cluster Dataset
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#transfer_contig_hits Contig
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#transfer_contig_to_cluster Dataset
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#transfer_contigs Dataset
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#transfer_hit Contig
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#transfer_n_contigs_def_hit_type Dataset
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#tree Feature
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#tree Gff_dataset
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#type Dataset
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#type Contig
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#type Hsp
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#type Hit
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#type Feature
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#var SNP
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#void_contig Rebuild
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#web_body Rebuild
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#web_header Rebuild
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#within? Hsp
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#write Feature
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#write_gbrowse_gff Rebuild
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#write_model_fasta Rebuild
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#zygosity SNP