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• Introduction to CLC Main Workbench
  • Contact information and citation
  • Download and installation
    • Program download
    • Installation on Microsoft Windows
    • Installation on macOS
    • Installation on Linux with an installer
  • System requirements
    • Limitations on maximum number of cores
  • Workbench Licenses
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Upgrade license
    • Configure license server connection
    • Download a static license on a non-networked machine
    • Viewing mode
    • Start in safe mode
  • Plugins
    • Install
    • Uninstall
    • Updating plugins
  • Network configuration
  • CLC Server connection
  • Getting started and latest improvements
• User interface
  • View Area
    • Open view
    • History and Element Info views
    • Close views
    • Save changes in a view
    • Undo/Redo
    • Arrange views in View Area
    • Moving a view to a different screen
    • Side Panel
  • Zoom and selection in View Area
    • Zoom in
    • Zoom out
    • Selecting, panning and zooming
  • Toolbox and Favorites tabs
    • Toolbox tab
    • Favorites tab
  • Processes tab and Status bar
  • Workspace
  • List of shortcuts
• Data management and search
  • Navigation Area
    • Data structure
    • Create new folders
    • Sorting folders
    • Multiselecting elements
    • Moving and copying elements
    • Change element names
    • Delete, restore and remove elements
    • Show folder elements in a table
  • Working with tables
    • Filtering tables
  • Customized attributes on data locations
    • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching
  • Local search
    • Quick search
    • Advanced search
• User preferences and settings
  • General preferences
  • View preferences
    • Import and export Side Panel settings
  • Data preferences
  • Advanced preferences
  • Export/import of preferences
  • View settings for the Side Panel
• Printing
  • Selecting which part of the view to print
  • Page setup
  • Print preview
• Import/export of data and graphics
  • Standard import
    • External files
  • Data export
    • Export formats
    • Export parameters
    • Specifying the exported file name(s)
    • Export of folders and data elements in CLC format
    • Export of dependent elements
    • Export of tables
    • JSON export
    • Graphics export
    • Export history
    • Backing up data from the CLC Workbench
  • Export graphics to files
    • File formats
  • Export graph data points to a file
  • CLC Server data import and export
  • Copy/paste view output
• Data download
  • Search for Sequences at NCBI
    • NCBI search options
    • Handling of NCBI search results
  • Search for PDB Structures at NCBI
    • Structure search options
    • Handling of NCBI structure search results
    • Save structure search parameters
  • Search for Sequences in UniProt (Swiss-Prot/TrEMBL)
    • UniProt search options
    • Handling of UniProt search results
    • Save UniProt search parameters
  • Sequence web info
• Running tools, handling results and batching
  • Running tools
    • Running a tool on a CLC Server
  • Handling results
  • Batch processing
    • Standard batch processing
    • Batch overview
    • Parameters for batch runs
    • Running the analysis and organizing the results
• Metadata
  • Creating metadata tables
    • Importing metadata
    • Creating a metadata table directly in the Workbench
  • Associating data elements with metadata
    • Associate Data Automatically
    • Associate Data with Row
  • Working with data and metadata
    • Finding data elements based on metadata
    • Viewing metadata associations
    • Removing metadata associations
    • Identifying metadata rows without associated data
  • Moving, copying and exporting metadata
  • Editing Metadata tables
• Workflows
  • Creating a workflow
    • Adding elements to a workflow
    • Connecting workflow elements
    • Ordering inputs
    • Validating a workflow
  • Editing existing workflows
    • Snippets in workflows
    • Workflow visualization
  • Workflow elements
    • Anatomy of workflow elements
    • Workflow element coloring
    • Basic configuration of workflow elements
    • Configuring input and output elements
    • Track lists as workflow outputs
    • Input modifying tools
  • Launching workflows individually and in batches
    • Importing data on the fly
    • Workflow outputs and workflow result metadata tables
    • Running workflows in batch mode
    • Batching workflows with more than one input changing per run
  • Batching part of a workflow
    • Iterate
    • Collect and Distribute
    • Running part of a workflow multiple times
  • Advanced workflow batching
    • Multiple levels of batching
    • Splitting paths in a workflow
    • Matching up inputs with each other and analyzing them together later in the workflow
  • Managing workflows
    • Updating workflows
    • Creating a workflow installation file
    • Installing a workflow
• Other data types
  • Tracks
• Viewing and editing sequences
  • View sequence
    • Sequence settings in Side Panel
    • Selecting parts of the sequence
    • Editing the sequence
    • Sequence region types
  • Circular DNA
    • Using split views to see details of the circular molecule
    • Mark molecule as circular and specify starting point
  • Working with annotations
    • Viewing annotations
    • Adding annotations
    • Edit annotations
    • Removing annotations
  • Element information
  • View as text
  • Sequence Lists
• 3D Molecule Viewer
  • Importing molecule structure files
    • From the Protein Data Bank
    • From your own file system
    • BLAST search against the PDB database
    • Import issues
  • Viewing molecular structures in 3D
  • Customizing the visualization
    • Visualization styles and colors
    • Project settings
  • Tools for linking sequence and structure
    • Show sequence associated with molecule
    • Link sequence or sequence alignment to structure
    • Transfer annotations between sequence and structure
  • Align Protein Structure
    • Example: alignment of calmodulin
    • The Align Protein Structure algorithm
  • Generate Biomolecule
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • View alignments
    • Bioinformatics explained: Sequence logo
  • Edit alignments
    • Realignment
  • Join alignments
  • Pairwise comparison
    • The pairwise comparison table
    • Bioinformatics explained: Multiple alignments
• Phylogenetic trees
  • K-mer Based Tree Construction
  • Create tree
  • Model Testing
  • Maximum Likelihood Phylogeny
    • Bioinformatics explained
  • Tree Settings
    • Minimap
    • Tree layout
    • Node settings
    • Label settings
    • Background settings
    • Branch layout
    • Bootstrap settings
    • Visualizing metadata
    • Node right click menu
  • Metadata and phylogenetic trees
    • Table Settings and Filtering
    • Add or modify metadata on a tree
    • Undefined metadata values on a tree
    • Selection of specific nodes
• General sequence analyses
  • Extract sequences
  • Shuffle sequence
  • Dot plots
    • Create dot plots
    • View dot plots
    • Bioinformatics explained: Dot plots
    • Bioinformatics explained: Scoring matrices
  • Local complexity plot
  • Sequence statistics
    • Bioinformatics explained: Protein statistics
  • Join Sequences
  • Pattern discovery
    • Pattern discovery search parameters
    • Pattern search output
  • Motif Search
    • Dynamic motifs
    • Motif search from the Toolbox
    • Java regular expressions
  • Create motif list
• Nucleotide analyses
  • Convert DNA to RNA
  • Convert RNA to DNA
  • Reverse complements of sequences
  • Translation of DNA or RNA to protein
  • Find open reading frames
    • Open reading frame parameters
• Protein analyses
  • Protein charge
  • Antigenicity
  • Hydrophobicity
    • Hydrophobicity graphs along sequence
    • Bioinformatics explained: Protein hydrophobicity
  • Download Pfam Database
  • Pfam domain search
  • Download 3D Protein Structure Database
  • Find and Model Structure
    • Create structure model
    • Model structure
  • Secondary structure prediction
  • Protein report
  • Reverse translation from protein into DNA
    • Bioinformatics explained: Reverse translation
  • Proteolytic cleavage detection
    • Bioinformatics explained: Proteolytic cleavage
• Sequencing data analyses and Assembly
  • Importing and viewing trace data
    • Trace settings in the Side Panel
  • Trim sequences
    • Trimming using the Trim tool
    • Manual trimming
  • Assemble sequences
  • Assemble sequences to reference
  • Sort sequences by name
  • Add sequences to an existing contig
  • View and edit contigs and read mappings
    • View settings in the Side Panel
    • Editing a contig or read mapping
    • Sorting reads
    • Read conflicts
    • Using the mapping
    • Extract reads from a mapping
    • Variance table
  • Reassemble contig
  • Secondary peak calling
  • Extract Consensus Sequence
  • Combine Reports
    • Combine Reports output
• Primers and probes
  • Primer design - an introduction
    • General concept
    • Scoring primers
  • Setting parameters for primers and probes
    • Primer Parameters
  • Graphical display of primer information
    • Compact information mode
    • Detailed information mode
  • Output from primer design
  • Standard PCR
    • When a single primer region is defined
    • When both forward and reverse regions are defined
    • Standard PCR output table
  • Nested PCR
  • TaqMan
  • Sequencing primers
  • Alignment-based primer and probe design
    • Specific options for alignment-based primer and probe design
    • Alignment based design of PCR primers
    • Alignment-based TaqMan probe design
  • Analyze primer properties
  • Find binding sites and create fragments
    • Binding parameters
    • Results - binding sites and fragments
  • Order primers
• Cloning and restriction sites
  • Restriction site analyses
    • Dynamic restriction sites
    • Restriction Site Analysis
  • Restriction enzyme lists
  • Molecular cloning
    • Introduction to the cloning editor
    • The cloning workflow
    • Manual cloning
    • Insert restriction site
  • Gateway cloning
    • Add attB sites
    • Create entry clones (BP)
    • Create expression clones (LR)
  • Gel electrophoresis
    • Gel view
• RNA structure
  • RNA secondary structure prediction
    • Selecting sequences for prediction
    • Secondary structure prediction parameters
    • Structure as annotation
  • View and edit secondary structures
    • Graphical view and editing of secondary structure
    • Tabular view of structures and energy contributions
    • Symbolic representation in sequence view
    • Probability-based coloring
  • Evaluate structure hypothesis
    • Selecting sequences for evaluation
    • Probabilities
  • Structure scanning plot
    • Selecting sequences for scanning
    • The structure scanning result
  • Bioinformatics explained: RNA structure prediction by minimum free energy minimization
    • The algorithm
    • Structure elements and their energy contribution
• Expression analysis
  • Experimental design
    • Setting up an experiment
    • Organization of the experiment table
    • Adding annotations to an experiment
    • Scatter plot view of an experiment
    • Cross-view selections
  • Transformation and normalization
    • Selecting transformed and normalized values for analysis
    • Transformation
    • Normalization
  • Quality control
    • Create Box Plot
    • Hierarchical Clustering of Samples
    • Principal Component Analysis
  • Feature clustering
    • Hierarchical clustering of features
    • K-means/medoids clustering
  • Statistical analysis - identifying differential expression
    • Empirical analysis of DGE
    • Tests on proportions
    • Gaussian-based tests
    • Corrected p-values
    • Volcano plots - inspecting the result of the statistical analysis
  • Annotation tests
    • Hypergeometric Tests on Annotations
    • Gene Set Enrichment Analysis
  • General plots
    • Histogram
    • MA plot
    • Scatter plot
• BLAST search
  • Running BLAST searches
    • BLAST at NCBI
    • BLAST against local data
  • Output from BLAST searches
    • Graphical overview for each query sequence
    • Overview BLAST table
    • BLAST graphics
    • BLAST HSP table
    • BLAST hit table
    • Extracting a consensus sequence from a BLAST result
  • Local BLAST databases
    • Make pre-formatted BLAST databases available
    • Download NCBI pre-formatted BLAST databases
    • Create local BLAST databases
  • Manage BLAST databases
  • Bioinformatics explained: BLAST
    • How does BLAST work?
    • Which BLAST program should I use?
    • Which BLAST options should I change?
    • Where can I get the BLAST+ programs
    • What you cannot get out of BLAST
    • Other useful resources
• Utility Tools
  • Batch Rename
  • Extract Annotations
• Legacy tools
  • Batch launching workflows with multiple inputs
• Appendix
  • Graph preferences
  • BLAST databases
    • Peptide sequence databases
    • Nucleotide sequence databases
    • Adding more databases
  • Proteolytic cleavage enzymes
  • Restriction enzymes database configuration
  • Technical information about modifying Gateway cloning sites
  • IUPAC codes for amino acids
  • IUPAC codes for nucleotides
  • Formats for import and export
    • List of bioinformatic data formats
    • List of graphics data formats
  • Gene expression annotation files and microarray data formats
    • GEO (Gene Expression Omnibus)
    • Affymetrix GeneChip
    • Illumina BeadChip
    • Gene ontology annotation files
    • Generic expression and annotation data file formats
  • Translation Tables
    • 1. Standard
    • 2. Vertebrate Mitochondrial
    • 3. Yeast Mitochondrial
    • 4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
    • 5. Invertebrate Mitochondrial
    • 6. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
    • 9. Echinoderm Mitochondrial; Flatworm Mitochondrial
    • 10. Euplotid Nuclear
    • 11. Bacterial and Plant Plastid
    • 12. Alternative Yeast Nuclear
    • 13. Ascidian Mitochondrial
    • 14. Alternative Flatworm Mitochondrial
    • 15. Blepharisma Macronuclear
    • 16. Chlorophycean Mitochondrial
    • 21. Trematode Mitochondrial
    • 22. Scenedesmus Obliquus Mitochondrial
    • 23. Thraustochytrium Mitochondrial
    • 24. Pterobranchia Mitochondrial
    • 25. Candidate Division SR1 and Gracilibacteria
  • Custom codon frequency tables
  • Matrices for alignment calculation
    • PAM30 log-odds matrix
    • PAM60 log-odds matrix
    • BLOSUM42 log-odds matrix
    • BLOSUM62 log-odds matrix
    • BLOSUM80 log-odds matrix
• Bibliography

List of shortcuts

The keyboard shortcuts available in CLC Main Workbench are listed below.

Action	Windows/Linux	macOS
Adjust selection	Shift + arrow keys	Shift + arrow keys
Adjust workflow layout	Shift + Alt + L	+ Shift + Alt + L
Back to Navigation Area	Alt + Home	+ Home
	or Alt + fn + left arrow	or + fn + left arrow
BLAST	Ctrl + Shift + L	+ Shift + L
BLAST at NCBI	Ctrl + Shift + B	+ Shift + B
Close	Ctrl + W	+ W
Close all views	Ctrl + Shift + W	+ Shift + W
Copy	Ctrl + C	+ C
Create alignment	Ctrl + Shift + A	+ Shift + A
Create track list	Ctrl + L	+ L
Cut	Ctrl + X	+ X
Delete	Delete	Delete or + Backspace
Exit	Alt + F4	+ Q
Export	Ctrl + E	+ E
Export graphics	Ctrl + G	+ G
Find Next Conflict	'.' (dot)	'.' (dot)
Find Previous Conflict	',' (comma)	',' (comma)
Help	F1	F1
Import	Ctrl + I	+ I
Launch tools	Ctrl + Shift + T	+ Shift + T
Maximize/restore View size	Ctrl + M	+ M
Move gaps in alignment	Ctrl + arrow keys	+ arrow keys
New Folder	Ctrl + Shift + N	+ Shift + N
New Sequence	Ctrl + N	+ N
Panning Mode	Ctrl + 4	+ 4
Paste	Ctrl + V	+ V
Print	Ctrl + P	+ P
Redo	Ctrl + Y	+ Y
Rename	F2	F2
Save	Ctrl + S	+ S
Save As	Ctrl + Shift + S	+ Shift + S
Scrolling horizontally	Shift + Scroll wheel	Shift + Scroll wheel
Search local data	Ctrl + Shift + F	+ Shift + F
Search via Side Panel	Ctrl + F	+ F
Search NCBI	Ctrl + B	+ B
Search UniProt	Ctrl + Shift + U	+ Shift + U
Select All	Ctrl + A	+ A
Select Selection Mode	Ctrl + 1 (one)	+ 1 (one)
Show folder content	Ctrl + O	+ O
Show/hide Side Panel	Ctrl + U	+ U
Sort folder	Ctrl + Shift + R	+ Shift + R
Split Horizontally	Ctrl + T	+ T
Split Vertically	Ctrl + J	+ J
Switch tabs in View Area	Ctrl + PageUp/PageDown	Ctrl + PageUp/PageDown
	or Ctrl + fn + arrow up/down	or Ctrl + fn + arrow up/down
Switch views	Ctrl + Shift + PageUp/arrow up	Ctrl + Shift + PageUp/arrow up
	Ctrl + Shift + PageDown/arrow down	Ctrl + Shift + PageDown/arrow down
Translate to Protein	Ctrl + Shift + P	+ Shift + P
Undo	Ctrl + Z	+ Z
Update folder	F5	F5
User Preferences	Ctrl + K	+ ,

Scroll and Zoom shortcuts

Action	Windows/Linux	macOS
Vertical scroll in reads tracks	Alt + Scroll wheel	Alt + Scroll wheel
Vertical scroll in reads tracks, fast	Shift+Alt+Scroll wheel	Shift+Alt+Scroll wheel
Vertical zoom in graph tracks	Ctrl + Scroll wheel	+ Scroll wheel
Zoom	Ctrl + Scroll wheel	+ Scroll wheel
Zoom In Mode	Ctrl + 2	+ 2
Zoom In (without clicking)	'+' (plus)	'+' (plus)
Zoom Out Mode	Ctrl + 3	+ 3
Zoom Out (without clicking)	'-' (minus)	'-' (minus)
Zoom to base level	Ctrl + 0	+ 0
Zoom to fit screen	Ctrl + 6	+ 6
Zoom to selection	Ctrl + 5	+ 5
Reverse zoom mode	press and hold Shift	press and hold Shift

Workflows related shortcuts

Action	Windows/Linux	macOS
Workflow, add element	Alt + Shift + E	Alt + Shift + E
Workflow, collapse if its expanded	Alt + Shift + '-' (minus)	Alt + Shift + '-'
Workflow, create installer	Alt + Shift + I	Alt + Shift + I
Workflow, execute	Ctrl + enter	+ enter
Workflow, expand if its collapsed	Alt + Shift + '+' (plus)	Alt + Shift + '-'
Workflow, highlight used elements	Alt + Shift + U	Alt + Shift + U
Workflow, remove all elements	Alt + Shift + R	Alt + Shift + R

Combinations of keys and mouse movements

Action	Windows/Linux	macOS	Mouse movement
Maximize View			Double-click the tab of the View
Restore View			Double-click the View title
Reverse zoom mode	Shift	Shift	Click in view
Select multiple elements not grouped together	Ctrl		Click elements
Select multiple elements grouped together	Shift	Shift	Click elements
Select Editor and highlight the corresponding element in the Navigation Area	Alt or Ctrl		Click tab

"Elements" in this context refers to elements and folders in the Navigation Area selections on sequences, and rows in tables.

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