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User Guide to MegAlign Pro — 17.4
  • 17.4
Table of Contents
Home Page
  • User Guide to MegAlign Pro — 17.4
    • User Guide to MegAlign Pro — 17.4
  • Welcome to MegAlign Pro
    • Sequence alignment vs. sequence assembly
  • MegAlign Pro Tutorials
  • Create or Open a Project
    • Open an existing MegAlign Pro project
    • Create a new MegAlign Pro project
    • Import an alignment from another application
    • 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
        • Distance metric options
        • Gap treatment options
      • Tree view
      • Text view
      • Table view
      • Variants view
    • Panels
      • Explorer panel
        • Trees section
      • Style panel
        • Overview section
        • Sequence section
        • Multiple Alignment section
          • Available color schemes
        • Pairwise Alignment section
        • Distance section
        • 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
  • Customize the Look and Layout
    • Customize the appearance and layout of views
    • Customize the layout of other window components
    • Save the layout and apply it to other projects
  • Sequences
    • Add ungapped sequences to a project
    • Add gapped sequences to a project
    • Add only sequences that meet filtering thresholds
    • Add multi-segment sequences to a project
      • Try it! – Add and align multi-segment sequences
    • Add only the portion of sequence that corresponds to a feature
    • Add sequences from a saved project to an active project
    • Specify a reference sequence
    • 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
    • Advantages of using SeqNinja files
  • Tracks
    • Ruler tracks
    • Features tracks
    • Reference 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
    • Move the cursor to a specific position
    • Search for or within a sequence using a text query
    • Search for nucleotide or residue strings
    • Search for disagreements between sequences
  • 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 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
    • Detect and remove outliers from the alignment
    • 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
  • Visually Compare Other Sequences to One Sequence
  • Perform a Pairwise Alignment
    • Choosing a pairwise alignment method
    • 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
    • Generate a phylogenetic tree
    • Try it! – Determine the strain of an experimental viral genome sample
    • Work with multiple trees
    • Reroot a tree
    • Import a Newick-format tree
  • Trim an Alignment
  • Compute Variants
  • Copy, Paste and Delete
  • Export
    • Export an image of the view
    • Export data to a file
    • Export the alignment report
    • 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
    • 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
Download as PDF

Sequences

You can add the following types of sequences to a MegAlign Pro project:

  • Ungapped sequences, including SeqNinja files
  • Gapped sequences
  • Only sequences that meet filtering thresholds
  • Multi-segment sequences
  • Only the portion of a sequence that corresponds to a feature
  • Sequences from a saved MegAlign Pro project

The following video showcases several different ways to add sequences to a MegAlign Pro project:


Once sequences have been added, you can:

  • Specify a reference sequence
  • Manually specify sequence type (DNA, RNA, protein)
  • Reorder sequences
  • Rename sequences manually or automatically, using specified data fields
  • Reverse complement sequences
  • Trim an individual sequence
  • Remove sequences from a project
Save the layout and apply it to other projects
Add ungapped sequences to a project

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