Index

Symbols

--absolute_retrain command line option --color command line option --evaluate command line option --expand_slope command line option --extra_dna command line option --file_prefix command line option --groups command line option --help command line option --ignore_annotations command line option --include_all_repeats command line option --include_annotations command line option --indir command line option --keep command line option --keep_dropped_predictions command line option --kmer_size command line option --kmers_type command line option, [1] --list command line option --log command line option --make_training_data command line option --metrics command line option --min_contig_size command line option --min_repeat_len command line option --nonprophage_genegaps command line option --number command line option --output_choice command line option --output_dir command line option

--phage_genes command line option --phmms command line option, [1] --quiet command line option --randomforest_trees command line option --retrain command line option --skip_search command line option --threads command line option, [1] --training_set command line option --use_taxonomy command line option --version command line option --window_size command line option -d command line option -e command line option -g command line option, [1] -h command line option -k command line option, [1] -l command line option -m command line option -n command line option -o command line option -p command line option -r command line option -t command line option, [1] -u command line option -v command line option -w command line option

C

command line option --absolute_retrain --color --evaluate --expand_slope --extra_dna --file_prefix --groups --help --ignore_annotations --include_all_repeats --include_annotations --indir --keep --keep_dropped_predictions --kmer_size --kmers_type, [1] --list --log --make_training_data --metrics --min_contig_size --min_repeat_len --nonprophage_genegaps --number --output_choice --output_dir --phage_genes --phmms, [1] --quiet --randomforest_trees --retrain --skip_search --threads, [1] --training_set --use_taxonomy --version --window_size -d -e -g, [1] -h -k, [1] -l -m -n -o -p -r -t, [1] -u -v -w infile

I

infile command line option