• Manuals

Browse the manual

• Introduction to CLC Genomics Workbench
  • Contact information
  • System requirements
    • Limitations on maximum number of cores
  • Licenses
    • Request an evaluation license
    • Download a license using a license order ID ID
    • Import a license from a file
    • Upgrade license
    • Configure license server connection
    • Download a static license on a non-networked machine
    • Limited mode
  • About CLC Workbenches
    • New program feature request
    • Getting help
    • CLC Sequence Viewer vs. Workbenches
  • When the program is installed: Getting started
    • Quick start
    • Import of example data
  • Plugins
    • Installing plugins
    • Uninstalling plugins
    • Updating plugins
    • Resources
  • Network configuration
  • Latest improvements
• User interface
  • View Area
    • Open view
    • Show element in another view
    • 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 Status Bar
    • Processes
    • Toolbox
    • Status Bar
  • Workspace
    • Create Workspace
    • Select Workspace
    • Delete 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
  • Customized attributes on data locations
    • Configuring which fields should be available
    • Editing lists
    • Removing attributes
    • Changing the order of the attributes
  • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching
  • Local search
    • What kind of information can be searched?
    • Quick search
    • Advanced search
    • Search index
• User preferences and settings
  • General preferences
  • Default view preferences
    • Number formatting in tables
    • Import and export Side Panel settings
  • Data preferences
  • Advanced preferences
    • Default data location
    • NCBI BLAST
  • Export/import of preferences
    • The different options for export and import
  • View settings for the Side Panel
    • Saving, removing and applying saved settings
• Printing
  • Selecting which part of the view to print
  • Page setup
    • Header and footer
  • Print preview
• Import/export of data and graphics
  • Standard import
    • Import using the import dialog
    • Import using drag and drop
    • Import using copy/paste of text
    • External files
  • Import tracks
  • Import high-throughput sequencing data
    • 454 from Roche Applied Science
    • Illumina
    • SOLiD from Life Technologies
    • Fasta read files
    • Sanger sequencing data
    • Ion Torrent PGM from Life Technologies
    • Complete Genomics
    • General notes on handling paired data
    • SAM and BAM mapping files
  • Data export
    • Export of folders and multiple elements in CLC format
    • Export of dependent elements
    • Export history
    • The CLC format
    • Backing up data from the CLC Workbench
    • Export of workflow output
  • Export graphics to files
    • Which part of the view to export
    • Save location and file formats
    • Graphics export parameters
    • Exporting protein reports
  • Export graph data points to a file
  • Copy/paste view output
• History log
  • Element history
    • Sharing data with history
• Batching and result handling
  • Batch processing
    • Batch overview
    • Batch filtering and counting
    • Setting parameters for batch runs
    • Running the analysis and organizing the results
  • How to handle results of analyses
    • Table outputs
    • Batch log
  • Working with tables
    • Filtering tables
• Workflows
  • Creating a workflow
    • Adding workflow elements
    • Configuring workflow elements
    • Locking and unlocking parameters
    • Connecting workflow elements
    • Input and output
    • Layout
    • Input modifying tools
    • Workflow validation
    • Workflow creation helper tools
    • Adding to workflows
    • Supported data flows
  • Distributing and installing workflows
    • Creating a workflow installation file
    • Installing a workflow
    • Workflow identification and versioning
    • Automatic update of workflow elements
  • Executing a workflow
• Viewing and editing sequences
  • View sequence
    • Sequence settings in Side Panel
    • Restriction sites in the 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
    • Graphical view of sequence lists
    • Sequence list table
    • Extract sequences from sequence list
• Data download
  • GenBank search
    • GenBank search options
    • Handling of GenBank search results
    • Save GenBank search parameters
  • UniProt (Swiss-Prot/TrEMBL) search
    • UniProt search options
    • Handling of UniProt search results
    • Save UniProt search parameters
  • Search for structures at NCBI
    • Structure search options
    • Handling of NCBI structure search results
    • Save structure search parameters
  • Download reference genome data
    • Selecting data types for download
  • Sequence web info
    • Google sequence
    • NCBI
    • PubMed References
    • UniProt
    • Additional annotation information
• BLAST search
  • Running BLAST searches
    • BLAST at NCBI
    • BLAST a partial sequence against NCBI
    • BLAST against local data
    • BLAST a partial sequence against a local database
  • Output from BLAST searches
    • Graphical overview for each query sequence
    • Overview BLAST table
    • BLAST graphics
    • BLAST 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
    • Migrating from a previous version of the Workbench
  • Bioinformatics explained: BLAST
    • Examples of BLAST usage
    • Searching for homology
    • How does BLAST work?
    • Which BLAST program should I use?
    • Which BLAST options should I change?
    • Explanation of the BLAST output
    • I want to BLAST against my own sequence database, is this possible?
    • What you cannot get out of BLAST
    • Other useful resources
• 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
    • Moving and rotating
  • Customizing the visualization
    • Visualization styles and colors
    • Project settings
  • Snapshots of the molecule visualization
  • Sequences associated with the molecules
  • Troubleshooting 3D graphics errors
  • Updating old structure files
  • Protein structure alignment
    • The Align Protein Structure dialog box
    • Example: alignment of calmodulin
    • The Align Protein Structure algorithm
• General sequence analyses
  • Extract Annotations
  • Extract sequences
  • Shuffle sequence
  • Dot plots
    • Create dot plots
    • View dot plots
  • Bioinformatics explained: Dot plots
    • Realization of dot plots
    • Examples and interpretations of dot plots
  • Bioinformatics explained: Scoring matrices
    • Different scoring matrices
    • Use of 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
  • Reverse sequence
  • Translation of DNA or RNA to protein
    • Translate part of a nucleotide sequence
  • Find open reading frames
    • Open reading frame parameters
• Protein analyses
  • Signal peptide prediction
    • Signal peptide prediction parameter settings
    • Signal peptide prediction output
  • Bioinformatics explained: Prediction of signal peptides
    • Why the interest in signal peptides?
    • Different types of signal peptides
    • Prediction of signal peptides and subcellular localization
    • The SignalP method
    • What do the SignalP scores mean?
  • Protein charge
    • Modifying the layout
  • Transmembrane helix prediction
  • Antigenicity
    • Plot of antigenicity
    • Antigenicity graphs along sequence
  • Hydrophobicity
    • Hydrophobicity plot
    • Hydrophobicity graphs along sequence
  • Bioinformatics explained: Protein hydrophobicity
    • Hydrophobicity scales
  • Pfam domain search
    • Download of Pfam database
    • Running Pfam Domain Search
  • Secondary structure prediction
  • Protein report
    • Protein report output
  • Reverse translation from protein into DNA
    • Reverse translation parameters
  • Bioinformatics explained: Reverse translation
    • The Genetic Code
    • Solving the ambiguities of reverse translation
  • Proteolytic cleavage detection
    • Proteolytic cleavage parameters
  • Bioinformatics explained: Proteolytic cleavage
• Primers
  • 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
    • Saving primers
    • Saving PCR fragments
    • Adding primer binding annotation
  • Standard PCR
    • User input
    • Standard PCR output table
  • Nested PCR
    • Nested PCR output table
  • TaqMan
    • TaqMan output table
  • Sequencing primers
    • Sequencing primers output table
  • 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
• Sequencing data analyses
  • Importing and viewing trace data
    • Scaling traces
    • Trace settings in the Side Panel
  • Trim sequences
    • Trimming using the Trim tool
    • Manual trimming
  • Assemble sequences
  • Sort Sequences By Name
  • Assemble sequences to reference
  • Add sequences to an existing contig
  • View and edit read mappings
    • View settings in the Side Panel
    • Editing the read mapping
    • Sorting reads
    • Read conflicts
    • Using the mapping
    • Extract parts of a mapping
    • Variance table
  • Reassemble contig
  • Secondary peak calling
• Cloning and cutting
  • 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)
  • Restriction site analysis
    • Dynamic restriction sites
    • Restriction site analysis from the Toolbox
  • Gel electrophoresis
    • Separate fragments of sequences on gel
    • Separate sequences on gel
    • Gel view
  • Restriction enzyme lists
    • Create enzyme list
    • View and modify enzyme list
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • View alignments
  • Bioinformatics explained: Sequence logo
    • Calculation of sequence logos
  • Edit alignments
    • Move residues and gaps
    • Insert gaps
    • Delete residues and gaps
    • Copy annotations to other sequences
    • Move sequences up and down
    • Delete, rename and add sequences
    • Realign selection
  • Join alignments
    • How alignments are joined
  • Pairwise comparison
    • Pairwise comparison on alignment selection
    • Pairwise comparison parameters
    • The pairwise comparison table
  • Bioinformatics explained: Multiple alignments
    • Use of multiple alignments
    • Constructing multiple alignments
• Phylogenetic trees
  • Phylogenetic tree features
  • Create 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
    • Metadata
    • Node right click menu
  • Metadata and Phylogenetic Trees
    • Table Settings and Filtering
    • Add or modify metadata
    • Unknown metadata values
    • Selection of specific nodes
• RNA structure
  • RNA secondary structure prediction
    • Selecting sequences for prediction
    • Structure output
    • Partition function
    • Advanced options
    • 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
• Trimming, multiplexing and sequencing quality control
  • Trim Sequences
    • Quality trimming
    • Adapter trimming
    • Length trimming
    • Trim output
  • Demultiplex reads
  • Sequencing data quality control
    • Report contents
    • Adapters
    • Running the quality control tool
  • Merge overlapping pairs
    • Using quality scores when merging
    • Report of merged pairs
• Tracks
  • Track lists
    • Zooming and navigating track views
    • Adding, removing and reordering tracks
    • Showing a track in a table
    • Open track from a track list in table view
    • Finding annotations on the genome
    • Extract sequences from tracks
    • Creating track lists in workflows
  • Retrieving reference data tracks
  • Merging tracks
  • Converting data to tracks and back
    • Convert to tracks
    • Convert from tracks
  • Annotate and filter tracks
    • Annotate with overlap information
    • Extract reads based on overlap
    • Filter annotations on name
    • Filter Based on Overlap
  • Creating graph tracks
• Read mapping
  • Map Reads to Reference
    • Selecting reads and reference
    • Including or excluding regions (masking)
    • Mapping parameters
    • Gap placement
    • Computational requirements
    • Reference Caching
  • Mapping output options
  • Mapping reports
    • Detailed mapping report
    • Summary mapping report
  • Color space
    • Sequencing
    • Error modes
    • Mapping in color space
    • Viewing color space information
  • Mapping result
    • Mapping table
    • View settings in the Side Panel
    • Overlapping paired reads
    • Find broken pair mates
  • Local realignment
    • Method
    • Realignment of unaligned ends
    • Guided Realignment
    • Multi-pass local realignment
    • Known Limitations
    • Computational Requirements
    • How to run the Local Realignment tool
  • Merge mapping results
  • Extract consensus sequence
  • Coverage analysis
    • Running the Coverage analysis tool
• Sample Reads
  • What is Sample Reads?
  • How to run Sample Reads
• Resequencing
  • Create Statistics for Target Regions
    • Running the Create Statistics for Target Regions
    • Coverage summary report
    • Per-region statistics
    • Coverage table
  • Variant Detectors - overview
    • Differences among the variants called by the three variant callers
    • How the variant detectors work
  • Basic Variant Detection
  • Fixed Ploidy Variant Detection
    • Ploidy and sensitivity
  • Low Frequency Variant Detection
  • Variant Detectors - error model estimation
  • Variant Detectors - filters
    • General filters
    • Noise filters
  • Variant Detectors - the outputs
    • The variant track output
    • The annotated table output
    • The report
  • InDels and Structural Variants
    • How to run the InDels and Structural Variants tool
    • The Structural Variants and InDels output
    • The InDels and Structural Variants detection algorithm
    • The InDels and Structural Variants detection algorithm - Step 1: Creating Left- and Right breakpoint signatures
    • The InDels and Structural Variants detection algorithm - Step 2: Creating Structural variant signatures
    • Theoretically expected structural variant signatures
    • How sequence complexity is calculated
  • Variant data
    • Variant tracks
    • The annotated variant table
    • Variant types
    • Special notes upgrading to Genomics Workbench 7.5
  • Detailed information about overlapping paired reads
  • Annotate and filter variants
    • Filter against known variants
    • Annotating from known variants
    • Annotate with exon numbers
    • Annotate with flanking sequence
    • Filter marginal variant calls
    • Filter reference variants
  • Comparing variants
    • Compare variants within group
    • Compare sample variants
    • Fisher exact test
    • Trio analysis
    • Filter Against Control Reads
  • Predicting functional consequences
    • Amino acid changes
    • Predict splice site effect
    • GO enrichment analysis
    • Conservation score annotation
• Transcriptomics
  • RNA-Seq analysis
    • Specifying reads and reference
    • Tightly packed genes and genes in operons
    • Defining mapping options for RNA-Seq
    • Calculating expression values from RNA-Seq
    • Specifying RNA-Seq outputs
    • Interpreting the RNA-Seq analysis result
  • Small RNA analysis
    • Extract and count
    • Downloading miRBase
    • Annotating and merging small RNA samples
    • Working with the small RNA sample
    • Exploring novel miRNAs
  • Expression profiling by tags
    • Extract and count tags
    • Create virtual tag list
    • Annotate tag experiment
  • Experimental design
    • Setting up an experiment
    • Organization of the experiment table
    • Visualizing RNA-Seq read tracks for the experiment
    • Adding annotations to an experiment
    • Scatter plot view of an experiment
    • Cross-view selections
  • Working with tracks and experiments
    • Data structures for transcriptomics
  • Transformation and normalization
    • Selecting transformed and normalized values for analysis
    • Transformation
    • Normalization
  • Quality control
    • Creating box plots - analyzing distributions
    • Hierarchical clustering of samples
    • Principal component analysis
  • 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
  • Feature clustering
    • Hierarchical clustering of features
    • K-means/medoids clustering
  • Annotation tests
    • Hypergeometric tests on annotations
    • Gene set enrichment analysis
  • General plots
    • Histogram
    • MA plot
    • Scatter plot
• De novo sequencing
  • De novo assembly
    • How it works
    • Resolve repeats using reads
    • Automatic paired distance estimation
    • Optimization of the graph using paired reads
    • AGP export
    • Bubble resolution
    • Converting the graph to contig sequences
    • Summary
    • Randomness in the results
    • SOLiD data support in de novo assembly
    • De novo assembly parameters
    • De novo assembly report
  • Map reads to contigs
• Epigenomics
  • ChIP-Seq Analysis
    • Quality Control of ChIP-seq data
    • Learning peak shapes
    • Applying peak shape filters to call peaks
    • Running the ChIP-Seq Analysis tool
  • Annotate with nearby gene information
• Legacy tools
  • Quality-based variant detection
    • Assessing the quality of the neighborhood bases
    • Significance of variant
    • Ploidy and genetic code
    • Reporting the variants
  • Probabilistic variant detection
    • Calculation of the prior and error probabilities
    • Calculation of the likelihood
    • Calculation of the posterior probability for each site type at each position in the genome
    • Comparison with the reference sequence and identification of candidate variants
    • Posterior filtering and reporting of variants
    • Running the variant detection
    • Setting ploidy and genetic code
    • Reporting the variants found
  • ChIP-Seq Analysis (legacy)
    • Peak finding and false discovery rates
    • Read shifting
    • Peak refinement
    • Reporting the results
• Appendix
  • Comparison of workbenches
  • Use of multi-core computers
  • 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
  • SAM/BAM export format specification
    • Flags
  • 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
  • Comparison of track comparison tools
  • 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

Comparison of workbenches

Below we list a number of functionalities that differ between CLC Workbenches and the CLC Sequence Viewer:

• CLC Sequence Viewer ()
• CLC Main Workbench ()
• CLC Genomics Workbench ()

	Data handling	Viewer	Main	Genomics
	Add multiple locations to Navigation Area
	Share data on network drive
	Search all your data

	Assembly of sequencing data	Viewer	Main	Genomics
	Advanced contig assembly
	Importing and viewing trace data
	Trim sequences
	Assemble without use of reference sequence
	Map to reference sequence
	Assemble to existing contig
	Viewing and edit contigs
	Tabular view of an assembled contig (easy data overview)
	Secondary peak calling
	Multiplexing based on barcode or name

	Next-generation Sequencing Data Analysis	Viewer	Main	Genomics
	Import of 454, Illumina Genome Analyzer, SOLiD and Helicos data
	Reference assembly of human-size genomes
	De novo assembly
	SNP/DIP detection
	Graphical display of large contigs
	Support for mixed-data assembly
	Paired data support
	RNA-Seq analysis
	Expression profiling by tags
	ChIP-Seq analysis

	Expression Analysis	Viewer	Main	Genomics
	Import of Illumina BeadChip, Affymetrix, GEO data
	Import of Gene Ontology annotation files
	Import of Custom expression data table and Custom annotation files
	Multigroup comparisons
	Advanced plots: scatter plot, volcano plot, box plot and MA plot
	Hierarchical clustering
	Statistical analysis on count-based and gaussian data
	Annotation tests
	Principal component analysis (PCA)
	Hierarchical clustering and heat maps
	Analysis of RNA-Seq/Tag profiling samples

	Molecular cloning	Viewer	Main	Genomics
	Advanced molecular cloning
	Graphical display of in silico cloning
	Advanced sequence manipulation

	Database searches	Viewer	Main	Genomics
	GenBank Entrez searches
	UniProt searches (Swiss-Prot/TrEMBL)
	Web-based sequence search using BLAST
	BLAST on local database
	Creation of local BLAST database
	PubMed lookup
	Web-based lookup of sequence data
	Search for structures (at NCBI)

	General sequence analyses	Viewer	Main	Genomics
	Linear sequence view
	Circular sequence view
	Text based sequence view
	Editing sequences
	Adding and editing sequence annotations
	Advanced annotation table
	Join multiple sequences into one
	Sequence statistics
	Shuffle sequence
	Local complexity region analyses
	Advanced protein statistics
	Comprehensive protein characteristics report

	Nucleotide analyses	Viewer	Main	Genomics
	Basic gene finding
	Reverse complement without loss of annotation
	Restriction site analysis
	Advanced interactive restriction site analysis
	Translation of sequences from DNA to proteins
	Interactive translations of sequences and alignments
	G/C content analyses and graphs

	Protein analyses	Viewer	Main	Genomics
	3D molecule view
	Hydrophobicity analyses
	Antigenicity analysis
	Protein charge analysis
	Reverse translation from protein to DNA
	Proteolytic cleavage detection
	Prediction of signal peptides (SignalP)
	Transmembrane helix prediction (TMHMM)
	Secondary protein structure prediction
	PFAM domain search

	Sequence alignment	Viewer	Main	Genomics
	Multiple sequence alignments (Two algorithms)
	Advanced re-alignment and fix-point alignment options
	Advanced alignment editing options
	Join multiple alignments into one
	Consensus sequence determination and management
	Conservation score along sequences
	Sequence logo graphs along alignments
	Gap fraction graphs
	Copy annotations between sequences in alignments
	Pairwise comparison

	RNA secondary structure	Viewer	Main	Genomics
	Advanced prediction of RNA secondary structure
	Integrated use of base pairing constraints
	Graphical view and editing of secondary structure
	Info about energy contributions of structure elements
	Prediction of multiple sub-optimal structures
	Evaluate structure hypothesis
	Structure scanning
	Partition function

	Dot plots	Viewer	Main	Genomics
	Dot plot based analyses

	Phylogenetic trees	Viewer	Main	Genomics
	Neighbor-joining and UPGMA phylogenies
	Maximum likelihood phylogeny of nucleotides

	Pattern discovery	Viewer	Main	Genomics
	Search for sequence match
	Motif search for basic patterns
	Motif search with regular expressions
	Motif search with ProSite patterns
	Pattern discovery

	Primer design	Viewer	Main	Genomics
	Advanced primer design tools
	Detailed primer and probe parameters
	Graphical display of primers
	Generation of primer design output
	Support for Standard PCR
	Support for Nested PCR
	Support for TaqMan PCR
	Support for Sequencing primers
	Alignment based primer design
	Alignment based TaqMan probe design
	Match primer with sequence
	Ordering of primers
	Advanced analysis of primer properties

	Molecular cloning	Viewer	Main	Genomics
	Advanced molecular cloning
	Graphical display of in silico cloning
	Advanced sequence manipulation

	Virtual gel view	Viewer	Main	Genomics
	Fully integrated virtual 1D DNA gel simulator

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