Search - User Guide to MegAlign Pro - 18.0

Welcome to MegAlign Pro
- Sequence alignment vs. sequence assembly
MegAlign Pro Tutorials
Create or Open a Project
- Open an existing project
- Create a new project
- Create a new project containing translations of nucleotide sequences
- Import an alignment from another application
- Navigate between projects
MegAlign Pro Interface
- Welcome screen
- Views
- Panels
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 translations of nucleotide 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
- Edit gaps in a sequence
- 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
- Biophysics tracks
- Immunogenicity tracks
  - Antigenicity – Welling
  - Antigenicity – Jameson-Wolf
Features
- Map features (copy features to another sequence)
- Remove features
- Try it! – Map features
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 Sequence Matches
- Set up local BLAST databases
- Search for sequence matches using BLAST
- Search for text or accession number matches using Entrez
  - Filter text search results
- Access ID dialog
- Save and reopen saved search results
Choose the Alignment Type
Perform a Multiple Sequence Alignment
- Perform an initial multiple sequence alignment
- Modify a multiple alignment
- Unalign aligned sequences
- Try it! – Perform a Clustal Omega alignment
- 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
Perform a Gene Homology Alignment
- Reference Sequence screen
- Input Sequences screen
- Analysis Options screen
- Assembly Output screen
- Run Assembly Project screen
- Analyzing a gene homology alignment
Perform a Pairwise Sequence Alignment
- Pairwise alignment for sequences with similar lengths
- Pairwise alignment of a short sequence to a chromosome
- 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
- Try It! – Use Local pairwise alignment to find a gene within a genome
Trim an Alignment
Visually Compare Other Sequences to One Sequence
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
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

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