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User Guide to MegAlign Pro — 17.5
18.0
Table of Contents
Home Page
User Guide to MegAlign Pro — 17.5
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
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 protein sequence is selected
When a portion of a nucleotide 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
Biophysics tracks
Amphiphilicity (Eisenberg)
Charge Density (Lehninger)
Disorder (JRONN)
Hydropathy – Hopp-Woods
Hydropathy – Kyte-Doolittle
Hydropathy – Parker
Secondary Structure – Chou-Fasman
Secondary Structure – Deleage-Roux
Secondary Structure – Garnier-Robson
Stability – Aliphatic Index
Stability – Instability Index
Stability – Isoelectric Precipitate
Immunogenicity tracks
Antigenicity – Welling
Antigenicity – Jameson-Wolf
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 sequence alignment
Notes regarding multiple alignments
Troubleshooting “wrong type” or “too long” errors
Troubleshooting “fatal error” in Clustal Omega 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 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
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
Appendix
Save, Close and Exit
Turn off usage logging
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