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• Introduction to CLC Sequence Viewer
  • Contact information
  • Download and installation
    • Program download
    • Installation on Microsoft Windows
    • Installation on macOS
    • Installation on Linux with an installer
  • System requirements
    • CLC Sequence Viewer vs. Workbenches
  • When the program is installed: Getting started
    • Quick start
  • Plugins
    • Install
    • Uninstall
    • Updating plugins
  • Network configuration
  • Latest improvements
• User interface
  • 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
  • View Area
    • Open view
    • History and 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 Status Bar
    • Processes
    • Toolbox
    • Favorites
    • Status Bar
  • Workspace
  • List of shortcuts
  • Working with tables
    • Filtering tables
• User preferences and settings
  • General preferences
  • View preferences
    • Import and export Side Panel settings
  • 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 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 tables
  • Export graphics to files
    • File formats
  • Export graph data points to a file
  • Copy/paste view output
• Data download
  • Search for Sequences at NCBI
    • NCBI search options
    • Handling of NCBI search results
• 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
    • Removing annotations
  • Element information
  • View as text
  • Sequence Lists
• Viewing structures
  • Importing molecule structure files
  • 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
• General sequence analyses
  • Extract sequences
  • Shuffle sequence
  • Sequence statistics
    • Bioinformatics explained: Protein statistics
  • Join sequences
• Nucleotide analyses
  • Convert DNA to RNA
  • Convert RNA to DNA
  • Reverse complements of sequences
  • Reverse sequence
  • Translation of DNA or RNA to protein
  • Find open reading frames
    • Open reading frame parameters
• Restriction site analyses
  • Dynamic restriction sites
    • Manage enzymes
  • Restriction Site Analysis
  • Restriction enzyme lists
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • View alignments
  • Edit alignments
    • Delete and rename sequences
    • Bioinformatics explained: Multiple alignments
• Phylogenetic trees
  • Create tree
    • Bioinformatics explained
  • Tree Settings
    • Minimap
    • Tree layout
    • Node settings
    • Label settings
    • Background settings
    • Branch layout
    • Bootstrap settings
    • Node right click menu
• Appendix
  • More features
  • Graph preferences
  • Formats for import and export
    • List of bioinformatic data formats
    • List of graphics data formats
  • Restriction enzymes database configuration
  • IUPAC codes for amino acids
  • IUPAC codes for nucleotides
  • 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
  • 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

Sequence alignment

CLC Sequence Viewer can align nucleotides and proteins using a progressive alignment algorithm (see Bioinformatics explained: Multiple alignments.

This chapter describes how to use the program to align sequences, and alignment algorithms in more general terms.

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Subsections

• Create an alignment
• View alignments
• Edit alignments

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