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User Guide to MegAlign Pro — 17.1
  • 17.2
  • 17.1
  • 17.0
  • 16.0
  • 15.3
  • 15.2
Table of Contents
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  • User Guide to MegAlign Pro — 17.1
    • User Guide to MegAlign Pro — 17.2
    • User Guide to MegAlign Pro — 17.1
    • User Guide to MegAlign Pro — 17.0
    • User Guide to MegAlign Pro — 16.0
    • User Guide to MegAlign Pro — 15.3
    • User Guide to MegAlign Pro — 15.2
  • Welcome to MegAlign Pro
  • MegAlign Pro Tutorials
  • Create or Open a Project
    • Open an existing MegAlign Pro project
    • Create a new MegAlign Pro project
    • Create a new MegAlign Pro project based on a classic MegAlign project or gapped FASTA file
    • Navigate between projects
  • MegAlign Pro Interface
    • Welcome screen
    • Views
      • Overview
        • Overview prior to performing an alignment
        • Overview after aligning multiple genomes with Mauve
        • Overview after other alignments
        • Overview after aligning and entering additional sequences
        • Using the Overview as a sequence navigation tool
      • Sequences view
      • Pairwise view
      • Distance view
      • Tree view
      • Text view
      • Table view
      • Change the appearance of a view
      • Split and resize panes in a view
      • Zoom in or out on a view
    • Panels
      • Explorer panel
        • Trees section
      • Style panel
        • Overview section
        • Sequence section
          • Available color schemes
        • Multiple Alignment section
        • Pairwise Alignment section
        • Distance section
          • Distance metric options
          • Gap treatment options
        • Tree section
      • Tracks panel
        • Layout section
        • Options section
      • Features panel
      • Places panel
        • Favorites section
        • Recent section
      • Details panel
        • When no document, or a blank document, is open
        • When a non-empty document is open
        • When one sequence is selected
        • When a portion of a sequence is selected
        • When multiple sequences are selected
        • When a portion of multiple sequences is selected
        • When one track is selected
        • When multiple tracks are selected
        • When one feature is selected
        • When multiple features are selected
        • When a portion of a pairwise alignment is selected
      • Jobs panel
      • Console panel
    • Hide, show, move, or resize items in the MegAlign Pro window
  • Sequences
    • Add ungapped sequences to a project
      • Advantages of using SeqNinja files
    • Add gapped sequences to a project
    • Add multi-segment sequences to a project
      • Try it! – Add and align multi-segment sequences
    • Add sequences from a saved project to an active project
    • Manually specify sequence type
    • Change the order of sequences
    • Rename sequences manually
    • Rename sequences automatically using specified data fields
    • Reverse complement one or more sequences
    • Trim an individual sequence
    • Remove sequences from a project
  • Tracks
    • Ruler tracks
    • Features tracks
    • Consensus track
    • Consensus Match track
    • Sequence Logo track
    • GC Content track
    • Gap Fraction track
    • Numeric tracks
    • Match Bar track
    • Translation track
  • Features
    • Map features (copy features to another sequence)
      • Features screen
      • Options screen
      • Output screen
      • Output files
      • Mapping features in MegAlign Pro vs. SeqNinja
    • Remove features
    • Try it! – Map features
      • Part A: Add, rename and align sequences
      • Part B: Map a single feature
      • Part C: Map all features
      • Part D: Map a filtered set of features
      • Part E: Compare output files
      • Part F: Export the annotated target sequence
  • Search Within an Open Project
  • Make a Selection
  • Search for Sequences Online
    • Search for sequence matches (BLAST)
      • Search wizard: Query
      • Search wizard: Search
      • Search wizard: Options
      • Search wizard: Job
    • Search for text or accession number matches (Entrez)
    • Filter sequence search results
    • Filter text search results
    • Access ID dialog
  • Choose the Alignment Type
  • Perform a Multiple Alignment
    • Perform an initial multiple alignment
      • Notes regarding multiple alignments
      • Troubleshoot multiple alignments
    • Multiple alignment methods and options
      • Clustal Omega alignment options
      • Clustal W alignment options
      • MAFFT alignment options
      • MUSCLE alignment options
      • Mauve alignment options
    • Modify a multiple alignment
      • Subalign sequences
      • Merge two existing alignments (“Profile alignment”)
      • Merge unaligned sequences into an existing alignment
      • Align selected unaligned sequences with an existing alignment
    • Unalign aligned sequences
    • Try it! – Perform a Clustal Omega alignment
      • Part A: Add and align sequences
      • Part B: Navigate using the Overview
      • Part C: Change sequence names and rendering in the Sequences view
      • Part D: Change metrics and rendering in the Distance view
      • Part E: Change the appearance of the Tree view
    • Try it! – Perform a MUSCLE alignment with multi-segment sequences
      • Part A: Add and align multi-segment files
      • Part B: Replace a sequence in the Overview and view the phylogenetic tree
    • Try it! – Perform a genomic alignment with Mauve
      • Part A: Add genomic sequences using drag & drop
      • Part B: Perform a Mauve alignment using modified parameters
      • Part C: View a genomic alignment in the Overview
      • Part D: View the phylogenetic tree
  • Perform a Pairwise Alignment
    • Comparison of pairwise alignment methods
    • Substitution matrices
    • Try It! – Follow a multiple alignment with Global pairwise alignments
    • Try It! – Align transcripts to genes using Local and Global pairwise alignments
      • Part A: Compare results from three multiple alignment methods
      • Part B: Use a Local pairwise alignment method
      • Part C: Use a Global pairwise alignment method
    • Try It! – Use Local pairwise alignment to find a gene within a genome
  • Phylogenetic Trees
  • Trim an Alignment
  • Copy, Paste and Delete
  • Export
    • Export an image of the view
    • Export data to a file
    • Export data to MegAlign
    • Export a tree to a tree viewer
    • Retain custom names during export
    • Export data from the Text, Table or Pairwise views
  • Print Images
    • Change the default print size
  • Save, Close and Exit
  • Appendix
    • Turn off usage logging
    • Set preferences
      • Set application preferences
      • Set Internet preferences
      • Set temporary file preferences
    • Change the default application for opening files
    • Clean cached files on startup
    • Troubleshoot the error “A different version is running”
    • Supported file types
    • IUPAC codes
    • Installed Lasergene file locations
    • Research references

Export

The following topics discuss how to:

  • Export an image of the view
  • Export data to a file
  • Export data to MegAlign
  • Export a tree to a tree viewer
  • Export data from the Text, Table or Pairwise views

If you renamed sequences manually or automatically, learn how to retain custom names during export.

Copy, Paste and Delete
Export an image of the view

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