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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 Sequence Alignment » Modify 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 Sequence 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 Sequence 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 Sequence 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 Sequence 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. …

Save, Close and Exit

Save, Close and Exit

The following table describes how to save files, close projects and exit from MegAlign Pro: Task How to… Save all of the open projects simultaneously Choose File > Save All or press Ctrl/Cmd+Shift+S. Each project is saved with an .msa…

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,…

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…

Part B: Navigate using the Overview

Perform a Multiple Sequence 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…

Part D: View the phylogenetic tree

Perform a Multiple Sequence 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…

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 A: Add and align sequences

Perform a Multiple Sequence 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.…

Multiple sequence alignment methods and options

Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence alignment methods and options

MegAlign Pro offers both gene-level and genome-level multiple sequence alignment algorithms. (Gene homology alignments are covered in a separate topic.) Gene-level alignment of either protein or nucleotide sequences: In general, the three gene-level aligners have…

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…

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…

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,…

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…

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…

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 Sequence 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 Sequence 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 Sequence 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…

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.…

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…

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…

Generate a phylogenetic tree

Phylogenetic Trees » Generate a phylogenetic tree

MegAlign Pro offers three tree-building algorithms: Neighbor joining: BIONJ uses the BIONJ algorithm (Gascuel, 1997), a variant of the Neighbor-Joining algorithm (Saito and Nei, 1987) that was used in classic MegAlign. Choose this option if your project includes…

Part C: Use a Global pairwise alignment method

Perform a Pairwise Sequence 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…

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…

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…

Analysis Options screen

Perform a Gene Homology Alignment » Analysis Options screen

The Analysis Options wizard screen is the third of five screens used to set up a gene homology alignment. This screen allows you to customize options related to post-assembly analysis. You can leave all options at their default values or make custom selections, as…

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 >…

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…

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…

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…

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…

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…

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,…

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 Sequence 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…

Try It! – Follow a multiple alignment with Global pairwise alignments

Perform a Pairwise Sequence 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…

Part B: Use a Local pairwise alignment method

Perform a Pairwise Sequence 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…

Homologs view

MegAlign Pro Interface » Views » Homologs view

The Homologs view displays the results of a gene homology alignment. To access the view, perform a gene homology alignment. Then click on the Homologs tab or choose View > Homologs > Show. Use the dropdown menu at the top left of the view to choose whether to display…

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…

Make a Selection

Make a Selection

Depending on the view, you can select one or more sequences, any portion of a sequence, or a specific portion of sequence corresponding to a feature. The active selection is highlighted in light blue. The selection can then be copied to the clipboard, copied in a…

Variants view

MegAlign Pro Interface » Views » Variants view

To see the Variants view, you must first perform a multiple alignment. When the alignment is complete, the Variants view opens showing a Compute Variants button. Click the button to calculate the variants. If you have specified a reference sequence, variants are…

Create a new project

Create or Open a Project » Create a new project

There are a variety of ways to create a new MegAlign Pro project, whether a blank project, one that is prepopulated with sequences, or even one that is prepopulated and with the alignment already in progress. *Note: To create a new project and add automatic…

Input Sequences screen

Perform a Gene Homology Alignment » Input Sequences screen

The Input Sequences wizard screen is the second of five screens used to set up a gene homology alignment. This screen is used to add the sequences that you wish to align to the reference. Add sequences from your local computer or the Cloud using any of the four Add…

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…

Assembly Output screen

Perform a Gene Homology Alignment » Assembly Output screen

The Assembly Output wizard screen is the fourth of five screens used to set up a gene homology alignment. This screen requires you to specify a project name. You can also change the location for the alignment output. Project name – Type a name for the…

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…

Run Assembly Project screen

Perform a Gene Homology Alignment » Run Assembly Project screen

The Run Assembly Project wizard screen is the fourth of five screens used to set up a gene homology alignment. This screen is used to specify a location in which to save temporary files and to start the alignment. You can also review system memory information that will…

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…

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…

Reference tracks

Tracks » Reference tracks

MegAlign Pro provides the option to specify a reference sequence and then use it to guide a MAFFT alignment or act as the comparison sequence for variant analysis. By default, the reference sequence is displayed as a track in the Overview and/or Sequences view headers.…

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…

Set preferences

Appendix » Set preferences

To set preferences on Windows, choose Edit > Preferences. On Macintosh, choose MegAlign Pro > Preferences (macOS 12 and lower) or MegAlign Pro > Settings (macOS 13 and higher). Click any of the four items on the left to open the preferences dialog for that item, then…

Amphiphilicity (Eisenberg)

Tracks » Biophysics tracks » Amphiphilicity (Eisenberg)

The Amphiphilicity (Eisenberg) track predicts the Eisenberg Moment using the approach of Eisenberg et al., 1984. Hydrophobic moments are semi-empirical quantities based on computation and experimental measurements, which describe the distribution of hydrophilic and…

Specify a reference sequence

Sequences » Specify a reference sequence

This topic describes several reasons you might want to use a reference and procedures for specifying, changing, and removing the reference. Note that a reference sequence in MegAlign Pro is different from a reference in SeqMan Ultra or SeqMan NGen. In SeqMan NGen or…

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…

Reference Sequence screen

Perform a Gene Homology Alignment » Reference Sequence screen

The Reference Sequence wizard screen is the first of five screens used to set up a gene homology alignment. You must input at least one reference sequence here before proceeding. To add one or more sequences from your computer: To add local sequences, press Add…

Secondary Structure – Deleage-Roux

Tracks » Biophysics tracks » Secondary Structure – Deleage-Roux

The Secondary Structure – Deléage-Roux track predicts secondary structure using the approach of Deléage and Roux, 1987. The method uses an independent prediction of the protein’s structural class to bias the prediction of its secondary structure.…

Pairwise alignment for sequences with similar lengths

Perform a Pairwise Sequence Alignment » Pairwise alignment for sequences with similar lengths

The following instructions describe how to align sequences with similar lengths (i.e., within one or two orders of magnitude). DNASTAR has used these pairwise algorithms in this workflow to successfully align protein sequences up to 35,000 bases in length. *Note: If…

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…

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…

Secondary Structure – Garnier-Robson

Tracks » Biophysics tracks » Secondary Structure – Garnier-Robson

The Secondary Structure – Garnier-Robson track , from Garnier et al. (1978), Garnier and Robson (1990), and Garnier, Gibrat and Robson (1996), predicts protein structure from the amino acid sequence. The method examines the propensity of a given residue to…

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.…

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…

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…

Clustal W alignment options

Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence 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…

Part A: Add genomic sequences using drag & drop

Perform a Multiple Sequence 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…

Create a new project containing translations of nucleotide sequences

Create or Open a Project » Create a new project containing translations of nucleotide sequences

*Note: To create a new project and add sequences in their original formats, see the topic Create a new project. MegAlign Pro 17.6, released in 2024, can automatically translate selected nucleotide sequences (or subranges of those sequences) and add them to a new…

Analyzing a gene homology alignment

Perform a Gene Homology Alignment » Analyzing a gene homology alignment

After a gene homology alignment has finished, you can view the results in the: Tree view — The phylogenetic tree was automatically calculated according to the algorithm you specified in the Assembly Output screen and is ready to view. Homologs view — This…

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…

Pairwise alignment of a short sequence to a chromosome

Perform a Pairwise Sequence Alignment » Pairwise alignment of a short sequence to a chromosome

With the release of Lasergene 17.5 (July 2023), MegAlign Pro features a unique algorithm—adapted from one used in SeqMan NGen—that supports pairwise alignment of a short sequence (typically a cDNA) to a chromosome-length sequence. This type of alignment is…

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…

Merge unaligned sequences into an existing alignment

Perform a Multiple Sequence 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…

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…

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…

When a portion of a protein sequence is selected

MegAlign Pro Interface » Panels » Details panel » When a portion of a protein sequence is selected

When a portion of a protein 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 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…

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…