:Base ./bioedit.hlp
:Title BioEdit version 7.0.0 Help Contents
:Index BioEdit version 5.0.0 Help=bioedit.hlp
:Index Help Index=bioedit.fts
:Link ./Bioedit.HLP
1 BioEdit Contents on-screen=Main_Contents
1 BioEdit General Help Contents
2 About BioEdit
3 Introduction=intro
3 BioEdit version 7.0.0 features=features
3 Known problems / Limitations=limitations
3 General overview of program and program organization=general_overview
3 Contacting the Author=contact_author
2 General use of BioEdit
3 Sequence Editing / manipulation
4 Basic editing - selecting, sliding, edit box, on-screen editing
5 Manual alignment: Selecting and sliding residues=manual_alignment
5 Editing in an edit box=edit_box
5 Windowshading=windowshading
5 Adding a new sequence=adding_sequence
5 Editing on screen=editing_on_screen
5 Selecting sequences=selecting_sequences
5 Moving sequences=moving_sequences
5 Cut/Copy/Paste=cut_copy_paste
5 Minimizing an alignment=minimize_alignment
5 Searching functions=searching_functions
3 Basic manipulations / Sequence menu=basic_manipulations
3 Customizing the view=customizing_view
3 Customizing menu shortcuts=menu_shortcuts
3 Splitting the window view=split_window
3 Sorting Sequences=sorting_sequences
3 Feature annotations=feature_annotations
3 Sequence groups or families=sequence_groups
3 Verbal confirmation of sequences=verbal_readback
3 Valid residue characters vs non-residue characters=valid_residues
3 Locking a sequence to prevent accidental edits=edit_box
3 Comment lines=edit_box
3 File formats
4 File formats that BioEdit currently reads and writes=file_formats
4 Saving sequence annotation information=annotation_information
4 ABI autosequencer trace files=abi_files
4 Reading files in a Macintosh program=mac_files
2 Toggling between nucleotide and protein views=toggle_translation
2 Printing=printing
2 Exporting as raw text=export_text
2 Shaded graphic view of alignment=shaded_view
2 Restriction Maps=restriction_maps
2 Restriction Enzyme Browser=enzyme_browser
2 Codon tables=codon_tables
2 Six-frame translation=six_frame_translation
2 Drawing Plasmids=plasmid_drawing
2 Searching functions=searching_functions
2 Conservation plot view=conservation_plot
2 Anchoring a column=column_anchoring
2 Phylogenetic Tree Viewer=tree_viewer
2 Importing Phylogenetic Trees into an alignment=importing_trees
1 Basic Analysis Tools
2 Customizing External Accessories
3 Installing TreeView=installing_treeview
3 Adding and Configuring External Applications=configure_apps
3 Adding and Configuring a new Application=add_and_configure
3 Removing an Accessory Application=remove_accessory
3 Storage of Configuration Information=configuration_storage
3 An example: Configuring ClustalW to run through a custom BioEdit interface=configure_example
2 External Accessories
3 Adding and Configuring External Applications=configure_apps
3 BLAST Overview=blast
3 Local BLAST=local_blast
3 Creating a database=creating_database
3 Local BLAST searching=local_blast_searching
3 BLAST 2.0 client=blast_client
3 ClustalW
4 ClustalW Main Help=clustalw
4 General Info=general_clustalw_info
4 General help for CLUSTAL W=general_help_for_clustalw
4 Help for multiple alignments=multiple_alignments
4 Help for pairwise alignment parameters=pairwise_alignment_parameters
4 Help for multiple alignment parameters=multiple_alignment_parameters
4 Help for protein gap parameters=protein_gap_parameters
4 Help for output format options=output_options
4 Help for profile alignments=profile_alignments
4 Help for phylogenetic trees=phylogenetic_trees
4 Help for choosing protein weight matrix=protein_weight_matrix
4 Help for command line parameters=command_line_parameters
4 Help for tree output format options=output_format_options
4 Restriction mapping=restriction_mapping
4 Blast on the WWW=web_blast
4 Constructing World Wide Web bookmarks for BioEdit=constructing_bookmarks
2 Incorporated into BioEdit
3 Amino Acid and Nucleotide Composition=composition
3 Entropy Plots=entropy_plot
3 Hydrophobicity Profiles=hydrophobicity_profiles
3 Identity Matrix=identity_matrix
3 Positional nucleotide numerical summary=positional_summary
3 Search for conserved regions of an alignment=search_conserved
3 Dot Plot of two sequences=dot_plot
3 Pairwise sequence alignment=optimal_alignment
3 Nucleotide translation with codon usage=codon_usage
3 RNA comparative analysis
4 Covariation=covariation
4 Potential Pairings=potential_pairings
4 Mutual Information=mutual_information
4 Using Masks=masks
3 Setting preferences in BioEdit=setting_preferences