Method List
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#add_annotations GenbankManip
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#aln_hits RemoteNCBI
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#aln_hits SyntenyManip
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#build_multifasta BacterialComparator
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#cds_file GenbankManip
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#choose_best_hit SyntenyManip
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#coding_seq GenbankManip
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#concat_alignments BacterialComparator
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#cumulate_annotation_stats_reference BacterialAnnotator
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#db RemoteNCBI
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#extract_blast_results RemoteNCBI
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#extract_externaldb_prot_info BacterialAnnotator
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#extract_hits_dna SyntenyManip
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#extract_hits_prodigal SyntenyManip
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#extract_syntenic_fasta BacterialComparator
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#fasta_file FastaManip
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#fasta_flat FastaManip
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#finish_annotation BacterialAnnotator
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#gbk GenbankManip
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#genomes_list BacterialComparator
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#get_annotation_for_contig SyntenyManip
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#get_cds GenbankManip
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#get_ref_prot BacterialComparator
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#get_rna GenbankManip
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#get_sequence_from_flatfile BacterialComparator
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#initialize GenbankManip
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#initialize SyntenyManip
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#initialize BacterialComparator
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#initialize BacterialAnnotator
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#initialize RemoteNCBI
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#initialize FastaManip
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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 FastaManip
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#print_stats BacterialAnnotator
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#prodigal_files FastaManip
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#prune_aln_hits SyntenyManip
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#query_file SyntenyManip
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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 GenbankManip
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#run_annotation BacterialAnnotator
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#run_blat SyntenyManip
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#run_prodigal FastaManip
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#save_genbank_to_file GenbankManip
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#split_fasta FastaManip
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#split_genbank FastaManip
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#stats BacterialComparator
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#subject_file SyntenyManip
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#submit_blast RemoteNCBI
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#validate_output RemoteNCBI
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#write_cds_to_file GenbankManip
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#write_rna_to_file GenbankManip
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#xmloutput RemoteNCBI