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Related topics are listed below.
Customize the Look and Layout
Customize the Look and Layout
The following topics describe the many ways you can customize the look and layout of MegAlign Pro. Use the Style panel to change the look of a view (font styles and sizes, colors, number of decimal places, etc.) Customize the appearance and layout of…
Customize the appearance and layout of views
Customize the Look and Layout » Customize the appearance and layout of views
The following table lists ways in which you can customize the appearance and layout of views. Task How to… Show a view Use View > (View Name) > Show. Change the style (fonts, colors, calculation metrics and more) Use…
Customize the layout of other window components
Customize the Look and Layout » Customize the layout of other window components
Controls for this application’s view, panels and expand bars are described in the following table. For information that pertains only to views, also see Customize the appearance and layout of views. Task “How To” Show or open a hidden…
Detect and remove outliers from the alignment
Perform a Multiple Alignment » Detect and remove outliers from the alignment
After performing a multiple sequence alignment, you may wish to detect and remove outliers from the alignment. From the Distance view, select a reference sequence. Choose Distance > Order Sequences by Distance from Selection. By default, a heat map color scheme…
Part B: Replace a sequence in the Overview and view the phylogenetic tree
Perform a Multiple Alignment » Try it! – Perform a MUSCLE alignment with multi-segment sequences » Part B: Replace a sequence in the Overview and view the phylogenetic tree
In the Overview, look for the longest segment and the longest gap region (shown in gray) in each sequence. Note that both of these are located on the left for "Rat," and on the right for all the other groups. These clues indicate that the segments for "Rat" were likely…
Save the layout and apply it to other projects
Customize the Look and Layout » Save the layout and apply it to other projects
You can change the layout of MegAlign Pro’s views and panels as described in Customize the look and layout. Once you have arrived at a layout you like, you can save it and then apply it to future projects, either by default or only when you specify that it be…
Part D: Change metrics and rendering in the Distance view
Perform a Multiple Alignment » Try it! – Perform a Clustal Omega alignment » Part D: Change metrics and rendering in the Distance view
The Distance view shows a matrix (i.e., table) of numbers representing distances between each pair of sequences. Sequence distances are used as input in creating the Tree view, which you will explore in Part E. Selections within this view are synchronized with other…
Part C: Change sequence names and rendering in the Sequences view
Perform a Multiple Alignment » Try it! – Perform a Clustal Omega alignment » Part C: Change sequence names and rendering in the Sequences view
In Part B, you looked at the Sequences view while learning the function of the "viewport." You will now explore the Sequences view in more depth. The Sequences view displays entered sequences and aligned sequences. Sequences selected in this view are simultaneously…
Part E: Change the appearance of the Tree view
Perform a Multiple Alignment » Try it! – Perform a Clustal Omega alignment » Part E: Change the appearance of the Tree view
The Tree view shows evolutionary relationships predicted from the multiple sequence alignment. Click on the Tree tab at the bottom of the MegAlign Pro window. Press Neighbor Joining: BIONJ and then OK to calculate the tree. The Tree view is calculated using…
Choose the Alignment Type
Choose the Alignment Type
Which is better, multiple or pairwise alignment? This question is difficult to answer because it very much depends on how the alignment is going to be used. Mechanistically, the best sequence alignment is the one that produces the fewest number of mismatches. That…
Export the alignment report
Export » Export the alignment report
To export the alignment report for the selected block from a Mauve alignment, use File > Export Data > Alignment Report. To export the report for any other alignment type, use File > Export Data > Alignment Report. In both cases, the report is saved as a .txt file. …
Copy, Paste and Delete
Copy, Paste and Delete
In many cases, once you have selected text, data, sequences or subsequences, you can copy the information to the clipboard. *Note: Copy functions are limited by application memory and operating system buffer size. Therefore, for very long sequences or subsequences,…
Save, Close and Exit
Save, Close and Exit
To save, close, or exit: The following table describes how to save files, close projects and exit from MegAlign Pro: Task How to… To save all of the open projects simultaneously Choose File > Save All or press Ctrl/Cmd+Shift+S.…
Change the default print size
Print Images » Change the default print size
Unless otherwise specified on your computer, the default printing size for all DNASTAR applications is “U.S. Letter” size (8.5 × 11 inches = 21.6 × 28 cm). You can temporarily change to another size, such as A4, from within the application. However, the…
Change the order of sequences
Sequences » Change the order of sequences
Whether preparing an image of a view for publication, or simply for ease of analysis, you may want to change the order of sequences in one or more views. For instance, you may wish to order the tree to create a pleasing image or to draw the viewer’s focus to a…
Multiple alignment methods and options
Perform a Multiple Alignment » Multiple alignment methods and options
MegAlign Pro offers both gene-level and genome-level multiple alignment algorithms. Gene-level alignment of either protein or nucleotide sequences: In general, the three gene-level aligners have higher accuracy than the genome-level (Mauve) aligner. They offer…
Part B: Navigate using the Overview
Perform a Multiple Alignment » Try it! – Perform a Clustal Omega alignment » Part B: Navigate using the Overview
Observe that the sequence blocks in the Overview are now the same lengths. Sequence gaps are represented by gray coloring within the blocks. The light blue vertical column shown at the left of the green blocks, above, is a "viewport" showing which region is…
Export an image of the view
Export » Export an image of the view
To export an image of a view : Choose File > Export Image > (View Name) or click the Export image tool ( ) at the upper right of a view that allows exporting. Specify the file name and choose the export format: Adobe PDF (.pdf), Microsoft…
Part D: View the phylogenetic tree
Perform a Multiple Alignment » Try it! – Perform a genomic alignment with Mauve » Part D: View the phylogenetic tree
*Note: The images in this section show examples of how the trees might appear. Your trees may have different arrangements or different branch lengths from the ones shown. The current names of each sequence originated from the accession numbers that were embedded in…
Part A: Add and align sequences
Perform a Multiple Alignment » Try it! – Perform a Clustal Omega alignment » Part A: Add and align sequences
In this part of the tutorial, you will be adding 143 DNA sequences to the MegAlign Pro project and aligning them with the Clustal Omega algorithm using the default settings. If you have not yet downloaded and extracted the tutorial data, click here to download it.…
Part F: Export the annotated target sequence
Features » Try it! – Map features » Part F: Export the annotated target sequence
In MegAlign Pro, hover over any target sequence annotation to read the entry. Verify that the sample entry matches your search criteria by checking the following: Is the feature a CDS? Does its original note contain the letters “RB”? Also observe…
Change the default application for opening files
Appendix » Change the default application for opening files
Windows 7 and Windows 8: Open the Control Panel. Go to Programs > Default Programs > Associate a file type or protocol with a specific program. Select extension you wish to change in the Extensions list and then click the Change program button. Click the…
Move the cursor to a specific position
Search » Move the cursor to a specific position
To go to a specified position: Choose Edit > Go To (Pairwise) Position, use Ctrl/Cmd+J. If the project contains only aligned or only unaligned sequences, type in a number and click OK. If the project contains a mixture of aligned and unaligned sequences,…
Part A: Add, rename and align sequences
Features » Try it! – Map features » Part A: Add, rename and align sequences
Before mapping features in MegAlign Pro, you first need to add and align the sequences. If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. If a…
Overview after aligning and entering additional sequences
MegAlign Pro Interface » Views » Overview » Overview after aligning and entering additional sequences
The Overview has different appearances, depending on the stage and workflow. In all cases, sequences are represented as either gray or colored blocks. Any sequence that is not part of an alignment is shown in solid gray. After performing an alignment, any new…
Using the Overview as a sequence navigation tool
MegAlign Pro Interface » Views » Overview » Using the Overview as a sequence navigation tool
The light blue vertical column in the Overview is a “viewport” showing the region currently being displayed in the Sequences view. There are a number of methods—all performed within the Overview—for using the slider to navigate to a particular region in the…
Part C: View a genomic alignment in the Overview
Perform a Multiple Alignment » Try it! – Perform a genomic alignment with Mauve » Part C: View a genomic alignment in the Overview
Once the alignment has finished, notice how the Overview has changed in response to the parameter change, including changes to the colors of the blocks, and differences in which blocks are hanging below the line (i.e., on the opposite strand). Locate the…
Export data from the Text, Table or Pairwise views
Export » Export data from the Text, Table or Pairwise views
The Export data tool ( ), located in the header above the Text, Table or Pairwise views, lets you export data from those views. This tool provides a choice of three options, one of which has four sub-options. Options include: Export Data > Matches…
Part A: Add and align multi-segment files
Perform a Multiple Alignment » Try it! – Perform a MUSCLE alignment with multi-segment sequences » Part A: Add and align multi-segment files
If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. If a MegAlign Pro project is already open, choose File > New Alignment Project > Blank Document.…
Troubleshoot the error “A different version is running”
Appendix » Troubleshoot the error “A different version is running”
If you receive the error “A different version of Lasergene is running” when you try to launch a Lasergene application, but another version of Lasergene actually isn’t running, there may be a lingering .state file from another version that needs to be…
Try it! – Add and align multi-segment sequences
Sequences » Add multi-segment sequences to a project » Try it! – Add and align multi-segment sequences
The following video tutorial describes how to add multi-segment sequences and then align them using the MUSCLE multiple alignment algorithm. If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file…
Add only the portion of sequence that corresponds to a feature
Sequences » Add only the portion of sequence that corresponds to a feature
This topic describes two methods that allow you to align only the portions of sequences the correspond to a particular gene or other feature. Other portions of the sequences are discarded or removed prior to alignment, making the alignment for that gene both faster and…
Try it! – Determine the strain of an experimental viral genome sample
Phylogenetic Trees » Try it! – Determine the strain of an experimental viral genome sample
In this tutorial, you will use MegAlign Pro to compare an experimental SARS-CoV-2 sample to references sequences from four SARS-CoV-2 strains in order to see which strain is present in the sample. This type of analysis can be used with any viral genome samples that…
Try It! – Align transcripts to genes using Local and Global pairwise alignments
Perform a Pairwise Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments
This three-part tutorial illustrates the utility of pairwise alignments when comparing mRNA transcripts to their cognate genes. This example begins with multiple alignments of the alcohol dehydrogenase (ADH) gene from Drosophila melanogaster and four mRNA transcript…
MegAlign Pro Interface
MegAlign Pro Interface
MegAlign Pro displays your sequences and results in customizable views and panels. The items displayed in the window, their locations, colors, fonts, etc. can all be changed to suit your preferences. To learn more, see the following topics: Welcome screen…
Views
MegAlign Pro Interface » Views
The left side of the MegAlign Pro window is comprised of one or more “views.” To learn more about the types of views and how to change their appearances, click the links below. View types: Overview Sequences view Pairwise view Distance view Tree…
Sequences view
MegAlign Pro Interface » Views » Sequences view
The Sequences View displays added sequences and aligned sequences. Sequence names selected in this view are simultaneously selected all other views in MegAlign Pro. Similarly, sequence names selected elsewhere will be highlighted in the Sequences View. To access the…
Pairwise view
MegAlign Pro Interface » Views » Pairwise view
The Pairwise view displays sequences after performing a pairwise alignment or a BLAST or Entrez database search. Sequence names selected in this view are simultaneously selected all other views in MegAlign Pro. Similarly, sequence names selected elsewhere will be…
Overview
MegAlign Pro Interface » Views » Overview
The Overview provides a way to navigate within the sequences, no matter what type of sequences or alignment is used. In the case of genomic alignments generated by Mauve, the Overview also allows you to explore the relationships between multiple aligned blocks.…
Distance view
MegAlign Pro Interface » Views » Distance view
The Distance view shows a matrix (i.e., table) of numbers representing distances computed for each pair of sequences for the selected aligned block. Sequence distances are used as input in creating the phylogenetic tree shown in the Tree view. Selections within the…
Console panel
MegAlign Pro Interface » Panels » Console panel
The Console panel displays information, messages and warnings about the operation in progress, or an operation that was recently performed. To display the console for a particular project: Click the tab with the project name, then open its console using the View >…
Generate a phylogenetic tree
Phylogenetic Trees » Generate a phylogenetic tree
To generate a new phylogenetic tree: Add sequences and perform a multiple alignment. Use any of the following methods to direct MegAlign Pro to create a tree using the algorithm you specify. For helpful advice on choosing the best tree for your data, see this…
Part C: Use a Global pairwise alignment method
Perform a Pairwise Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments » Part C: Use a Global pairwise alignment method
Since the Local pairwise alignment in Part B was not an improvement over the multiple alignments in Part A, you will now try a Global pairwise alignment. This type of alignment forces the ends of both sequences to be aligned. Click the gear icon on the Pairwise view…
Search for disagreements between sequences
Search » Search for disagreements between sequences
MegAlign Pro supports searching for positions where the same letter code does not occur in all sequences. This type of search looks only at IUPAC letter codes and ignores gaps. In other words, it will not look for positions in which one sequence has a letter code and…
Tracks
Tracks
“Tracks” are rows of information that can be displayed or hidden, as desired, in the Overview and Sequences view. Tracks can pertain to a header, footer, or individual sequence row. The following video provides a brief overview of how tracks are used in…
Trim an individual sequence
Sequences » Trim an individual sequence
Individual sequences in the project can be trimmed before or after alignment based on features or by direct selection. This is different from trimming the entire alignment, which affects all sequences in the project. To trim an individual sequence before or after…
Overview section
MegAlign Pro Interface » Panels » Style panel » Overview section
To access options affecting the Overview display, click on the Style panel expand bar entitled Overview, or choose View > Style > Overview. Task How to… Increase/decrease the amount of vertical space between sequence blocks Use the…
Phylogenetic Trees
Phylogenetic Trees
MegAlign Pro lets you create and display one or more phylogenetic trees for a multiple alignment. The trees can use different algorithms, or the same algorithm with different settings. To learn more, see the following topics: Generate a phylogenetic tree Get to…
Part E: Compare output files
Features » Try it! – Map features » Part E: Compare output files
When the mapping initiated in Part D is finished, click the hyperlink to the output directory. Open both All features_map_features_1_report.tsv and CDS-RB features_map_features_1_report.tsv in any suitable spreadsheet…
Search wizard: Options
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Options
The Options screen is the third of four screens in the BLAST Search wizard, and has two tabs: Selection and Matches. These tabs allow you to customize miscellaneous parameters relating to the BLAST search. Click the Selection tab to make it active. In the…
Features screen
Features » Map features (copy features to another sequence) » Features screen
The Features screen is the first wizard screen of the Map Features dialog, and allows you to choose the features you want to include or exclude in the mapping. *Note: This dialog is optional, and you may click Next, if desired, to skip to the next screen. However,…
Panels
MegAlign Pro Interface » Panels
Settings panels allow you to optimize the look, contents and layout of the MegAlign Pro window. To learn what can be done within each panel and the expandable “sections” within each panel, click the links…
Rename sequences automatically using specified data fields
Sequences » Rename sequences automatically using specified data fields
The following procedure lets you create labels for one or more selected sequences automatically, using specified fields such as sequence length, organism, or description. To rename sequences using specified data fields: Select one or more sequence names from any…
Perform an initial multiple sequence alignment
Perform a Multiple Alignment » Perform an initial multiple sequence alignment
To perform the initial multiple sequence alignment: Select three or more sequences to align, or select nothing if you want to align all sequences. (Note: If you choose just two sequences, or if only two are present, you will be prompted to instead do a pairwise…
Part B: Use a Local pairwise alignment method
Perform a Pairwise Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments » Part B: Use a Local pairwise alignment method
Now that you have finished Part A of the tutorial, this part shows how you can use a local pairwise alignment to resolve the correct mapping of the first intron in isoF and isoC. Click on Pairwise view tab. Look at the left drop-down menu at the top of the view…
Try It! – Follow a multiple alignment with Global pairwise alignments
Perform a Pairwise Alignment » Try It! – Follow a multiple alignment with Global pairwise alignments
This tutorial demonstrates a situation in which a pairwise alignment can help resolve a confusing placement of gaps within a multiple alignment. In this case, a multiple protein sequence alignment suggests that the protein sequence from a specific organism (Tupaia…
Pairwise Alignment section
MegAlign Pro Interface » Panels » Style panel » Pairwise Alignment section
To access options affecting the display of pairwise alignments in the Pairwise view, click on the Style panel expand bar entitled Pairwise Alignment, or choose View > Style > Pairwise Alignment. Task How To Specify the wrapping style for rows…
Tree view
MegAlign Pro Interface » Views » Tree view
The Tree view shows evolutionary relationships estimated from the multiple sequence alignment, and is calculated using the current tree-building algorithm and settings, and the currently-selected Distance metric. This view is only accessible after you have performed a…
Research references
Appendix » Research references
Chou PY and Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence." Advances in Enzymology 47: 45-148. Darling AE, Mau B, and Perna NT (2010). “progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss, and…
Tree section
MegAlign Pro Interface » Panels » Style panel » Tree section
To access options affecting the Tree view, click on the Style panel expand bar entitled Tree, or choose View > Style > Tree. Task How to… Specify the layout of the view Click on any of the four orientations to show the phylogenetic…
Tracks panel
MegAlign Pro Interface » Panels » Tracks panel
The Tracks panel lets you manage the tracks displayed in the Overview and the Sequences view. To open the Tracks panel: Click on the Tracks tab (). If the panel is not already visible, reveal it using any of the following methods: Choose View > Tracks > Tracks…
Advantages of using SeqNinja files
Sequences » Advantages of using SeqNinja files
SeqNinja is DNASTAR’s tool for advanced and batch editing of genome sequences and features. SeqNinja allows you to convert file formats, batch edit and export features, merge and split sequence data, and transfer features between genome versions, automating the…
Sequence section
MegAlign Pro Interface » Panels » Style panel » Sequence section
To access options affecting the Sequences view and Pairwise view, click on the Style panel expand bar entitled Sequences, or choose View > Style > Sequences. Task How to… Select font options for the ruler numbers in the view Use the…
Create a new project
Create or Open a Project » Create a new project
To create a new MegAlign Pro project: Do any of the following: From the Welcome tab, click New Project on the left. Then choose one of the options on the right: New blank alignment project – Opens an empty project window. New alignment…
Set preferences
Appendix » Set preferences
To set preferences, choose Edit > Preferences (Windows) or MegAlign Pro > Preferences (Macintosh). Click any of the four items on the left to open the preferences dialog for that item, then follow the steps in the sections below. After setting preferences, click Apply…
Remove features
Features » Remove features
While features can only be mapped when all sequences involved have been aligned, features can be removed from a sequence before or after aligning. Feature removal is not reversible, so use caution when removing features, especially those from non-consensus…
Distance section
MegAlign Pro Interface » Panels » Style panel » Distance section
The Distance section affects the appearance of the Distance view. To access this section, click on the Style panel expand bar entitled Distance, or choose View > Style > Distance. *Note: In Lasergene 17.1 and earlier, this section was used to specify distance…
Sequence alignment vs. sequence assembly
Welcome to MegAlign Pro » Sequence alignment vs. sequence assembly
Sequence alignment and sequence assembly are very different workflows, but the terms are often used incorrectly. Adding to the confusion, both workflows can involve an optional “reference” sequence, and both can use some of the same sequence file types.…
Work with multiple trees
Phylogenetic Trees » Work with multiple trees
What are dynamic trees and how do they differ from “snapshots?”: MegAlign Pro allows you to compare multiple phylogenetic trees generated using custom settings. The phylogenetic algorithm you choose dictates which customizations affect the tree and whether…
Overview after aligning multiple genomes with Mauve
MegAlign Pro Interface » Views » Overview » Overview after aligning multiple genomes with Mauve
The Overview has different appearances, depending on the stage and workflow. A Mauve genome alignment results in a set of locally colinear blocks (LCBs), each of which is a conserved region across multiple sequences. In MegAlign Pro, these may be referred to as…
When multiple features are selected
MegAlign Pro Interface » Panels » Details panel » When multiple features are selected
If two or more features have been selected in a track in the Overview or Sequences view, the Details panel contains the following information: Heading Number of features currently selected (in blue). Type – List of all feature types represented…
Part A: Add genomic sequences using drag & drop
Perform a Multiple Alignment » Try it! – Perform a genomic alignment with Mauve » Part A: Add genomic sequences using drag & drop
If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. If a MegAlign Pro project is already open, choose File > New Alignment Project. Otherwise, launch…
Clustal W alignment options
Perform a Multiple Alignment » Multiple alignment methods and options » Clustal W alignment options
The Clustal W algorithm is for gene level alignment of either protein or nucleotide sequences. To run a Clustal W alignment, select two or more sequences and choose Align > (Re)Align Using Clustal W. If you wish to change method options, instead choose Align > Align…
Print Images
Print Images
To print an image of any MegAlign Pro view, whether it is currently active or not: Choose File > Print or use Ctrl/Cmd+P. The Print Document dialog opens: Use the Printer drop-down menu to choose the desired printer from a list of available…
Favorites section
MegAlign Pro Interface » Panels » Places panel » Favorites section
The Favorites section is similar to the bookmarks folder for a web browser. It contains a list of previously-visited locations that you have decided you may wish to visit again. To access the Favorites section: Click on the Places panel expand bar entitled…
Recent section
MegAlign Pro Interface » Panels » Places panel » Recent section
When you perform a search for a gene or numerical sequence location using Edit > Go To Position, each found location is automatically stored in the Recent section. Access this section by clicking on the Places panel expand bar entitled “Recent,” or by choosing View…
Part C: Map all features
Features » Try it! – Map features » Part C: Map all features
In this part of the tutorial, you will map all features from the source sequence to the target sequence. Right-click on the name of the source (upper) sequence and select Features > Map Features to Bottom Sequence. The Map Features wizard launches. In the…
Merge unaligned sequences into an existing alignment
Perform a Multiple Alignment » Modify a multiple alignment » Merge unaligned sequences into an existing alignment
To merge unaligned sequences into the current project’s existing alignment: In contrast to the “Profile alignment” method, this method retains existing gaps, and adds new gaps, if necessary. Add sequences to the project and align some or all of…
Perform a Pairwise Alignment
Perform a Pairwise Alignment
This application supports local, global and semi-global pairwise alignment methods. Pairwise alignments can only be performed when two sequences, and only two sequences, have been selected. A common workflow is to first perform a multiple alignment on an entire group…
When a portion of multiple sequences is selected
MegAlign Pro Interface » Panels » Details panel » When a portion of multiple sequences is selected
When a portion of multiple aligned sequences has been selected (e.g., by triple-clicking on a feature, or by dragging across the consensus sequence with the mouse), the Details panel contains the following information: Heading Sequences –…
Add gapped sequences to a project
Sequences » Add gapped sequences to a project
To import gapped sequences from an existing MegAlign Pro file (.msa): The following procedures both remove gaps from the sequences and place the updated sequences in the “Unassembled Sequences” area of the project. Click on the Add Sequences button ( ) or…
Add multi-segment sequences to a project
Sequences » Add multi-segment sequences to a project
Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment sequences. By entering a group of sequences into MegAlign Pro using a special command, the entire data set will be concatenated end-to-end and treated as a…
Style panel
MegAlign Pro Interface » Panels » Style panel
The Style panel has expandable sections with options affecting the Overview, Sequences, Distance and Tree views, as well as multiple and pairwise alignments. To open the Style panel: Click on the Style tab (). If the panel is not already visible, reveal it using any…
Navigate between projects
Create or Open a Project » Navigate between projects
You can open multiple projects within a single instance of MegAlign Pro. Each project is displayed in a separate tab and is initially assigned a unique name (Untitled[#].msa). To make a project the active project: Click on its project tab. To open an additional…
When a portion of a sequence is selected
MegAlign Pro Interface » Panels » Details panel » When a portion of a sequence is selected
When a portion of a sequence has been selected in any view (e.g., by double-clicking on a feature, or by dragging across the sequence with the mouse) except the Pairwise view, the Details panel contains the following information: Heading …
Part B: Map a single feature
Features » Try it! – Map features » Part B: Map a single feature
In this part of the tutorial, you will map a single selected feature from the source sequence to the target sequence. In order to choose the appropriate mapping command, you will need to know where the source and target sequences appear in relation to one another in…
Multiple Alignment section
MegAlign Pro Interface » Panels » Style panel » Multiple Alignment section
To access options affecting the display of multiple alignments in the Sequences view, click on the Style panel expand bar entitled Multiple Alignment, or choose View > Style > Multiple Alignment. Task How To Designate the sequence to consider…
Jobs panel
MegAlign Pro Interface » Panels » Jobs panel
After initiating an NCBI BLAST or Entrez search, you can monitor its progress and download its eventual output from the Jobs panel. This panel is not visible in a project until you have started running at least one search. To open the Jobs panel: Do any of the…
Part D: Map a filtered set of features
Features » Try it! – Map features » Part D: Map a filtered set of features
In this example, you will map only CDS features which have a note containing the letters RB. Right-click on the name of the source (upper) sequence and select Features > Map Features to Bottom Sequence. The Map Features wizard launches. In the Features…
Substitution matrices
Perform a Pairwise Alignment » Substitution matrices
A substitution matrix describes the rate at which a nucleotide or amino acid changes to another nucleotide or amino acid over time. When performing a pairwise alignment, you can specify the desired substitution matrix in the (Pairwise) Alignment Options…
Welcome to MegAlign Pro
Welcome to MegAlign Pro
MegAlign Pro is Lasergene’s application for generating multiple and pairwise alignments of protein and/or nucleic acid sequences using your choice of alignment methods. Easily navigate between synchronized views with a click of a button, and rearrange views and…
Try it! – Perform a Clustal Omega alignment
Perform a Multiple Alignment » Try it! – Perform a Clustal Omega alignment
This tutorial will use the Clustal Omega algorithm to multiply align 143 DNA sequence files consisting of regional variations of the Human Papilloma Virus L1 gene (HPV-L1). HPV has affected humans for hundreds of thousands of years and is known to cause cervical…
When a portion of a pairwise alignment is selected
MegAlign Pro Interface » Panels » Details panel » When a portion of a pairwise alignment is selected
When a portion of a sequence has been selected in the Pairwise view (e.g., by double-clicking on a feature, or by dragging across the sequence with the mouse), the Details panel contains the following information: Heading Selected Region …
Try It! – Use Local pairwise alignment to find a gene within a genome
Perform a Pairwise Alignment » Try It! – Use Local pairwise alignment to find a gene within a genome
Consider the case of a researcher who is trying to investigate the role of a gene isolated from a yet-unsequenced Salmonella strain. This strain has already been demonstrated to be both copper and multi-drug resistant. As demonstrated in the following tutorial,…
Sequence Logo track
Tracks » Sequence Logo track
To display the Sequence Logo track: To display or hide the Sequence Logo track in the Sequences view footer, perform an alignment and then check or uncheck the Sequence Logo box in the Tracks panel. This box is only visible after performing an alignment. How…
Add only sequences that meet filtering thresholds
Sequences » Add only sequences that meet filtering thresholds
You can specify a group of sequences to add and then use filtering options to only add a subset of those to the project. To add only sequences that meet filtering thresholds: Open the filter dialog by doing any of the following: From the Welcome screen, select New…
Retain custom names during export
Export » Retain custom names during export
After using File > Rename or File > Rename with Fields, the custom names are only exported as part of the sequence data in certain cases. Raw data sequences imported into MegAlign are never modified in any way, and always retain their original names. The following…
Merge two existing alignments (“Profile alignment”)
Perform a Multiple Alignment » Modify a multiple alignment » Merge two existing alignments (“Profile alignment”)
To merge two existing alignments: A “profile alignment” occurs when you merge a MegAlign Pro alignment (.msa) that was saved earlier with the current project. Profile alignments merge two existing multiple alignments without removing any of the existing gaps.…
Export a tree to a tree viewer
Export » Export a tree to a tree viewer
To export a phylogenetic tree to a file: Use File > Export Data > Tree to export tree data in Newick (.newick) or Nexus (.nex, .nxs) formats . The saved file can be opened by several free and commercial evolutionary biology software programs. To set the default…
Comparison of pairwise alignment methods
Perform a Pairwise Alignment » Comparison of pairwise alignment methods
The three types of alignment—Local, Global and Semi-Global—are actually quite similar, although they can often produce very different results. All use a method called dynamic programming to find the best scoring alignment between two sequences.…