Method List
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#add_annotation_ref_synteny_prot SequenceAnnotation
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#add_annotations SequenceAnnotation
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#aln_hits SequenceSynteny
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#annotation_files SequenceFasta
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#build_multifasta BacterialComparator
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#cds_file SequenceAnnotation
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#choose_best_hit SequenceSynteny
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#coding_seq SequenceAnnotation
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#concat_alignments BacterialComparator
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#cumulate_annotation_stats_reference BacterialAnnotator
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#extract_externaldb_prot_info BacterialAnnotator
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#extract_hits SequenceSynteny
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#extract_hits_dna SequenceSynteny
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#extract_syntenic_fasta BacterialComparator
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#fasta_file SequenceFasta
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#fasta_flat SequenceFasta
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#finish_annotation BacterialAnnotator
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#gbk SequenceAnnotation
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#genomes_list BacterialComparator
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#get_annotation_for_contig SequenceSynteny
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#get_cds SequenceAnnotation
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#get_ref_prot BacterialComparator
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#get_rna SequenceAnnotation
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#get_sequences SequenceSynteny
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#initialize SequenceAnnotation
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#initialize BacterialComparator
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#initialize SequenceSynteny
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#initialize BacterialAnnotator
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#initialize SequenceFasta
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#load_genome_cds BacterialComparator
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#mafft_align BacterialComparator
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#mafft_align_all_dna BacterialComparator
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#mafft_align_all_pep BacterialComparator
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#mafft_aln BacterialComparator
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#parse_genbank_files BacterialAnnotator
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#prepare_files_for_annotation BacterialAnnotator
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#print_sequence_for_gbk SequenceFasta
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#print_stats BacterialAnnotator
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#prune_aln_hits SequenceSynteny
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#query_file SequenceSynteny
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#query_sequences SequenceSynteny
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#raxml_tree BacterialComparator
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#raxml_tree_dna BacterialComparator
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#raxml_tree_pep BacterialComparator
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#read_prot_synteny BacterialComparator
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#rna_file SequenceAnnotation
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#run_annotation BacterialAnnotator
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#run_blat SequenceSynteny
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#run_prodigal SequenceFasta
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#run_reference_synteny_prot BacterialAnnotator
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#save_genbank_to_file SequenceAnnotation
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sec2str Helper
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#split_fasta SequenceFasta
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#split_genbank SequenceFasta
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#stats BacterialComparator
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#subject_file SequenceSynteny
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#subject_sequences SequenceSynteny
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#write_cds_to_file SequenceAnnotation
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#write_rna_to_file SequenceAnnotation