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Welcome screen

MegAlign Pro Interface » Welcome screen

The Welcome “project” opens when you launch MegAlign Pro and is a central location for opening projects, searching NCBI databases, getting help, and much more. As you add projects, the Welcome “project” will remain as the leftmost tab unless you…

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…

When one track is selected

MegAlign Pro Interface » Panels » Details panel » When one track is selected

If a single track has been selected in the Overview or Sequences view, the Details panel contains the following information. Heading Type of track (in blue). Summary – Basic information about what is displayed in the selected…

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…

Perform a Pairwise Sequence Alignment

MegAlign Pro supports local, global, semi-global, and chromosome-based pairwise alignment methods, as well as a specialized proprietary method for aligning cDNAs or other short sequences to a chromosome. Click here for descriptions and a comparison of the different…

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.…

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 –…

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…

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…

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…

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…

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 …

When one feature is selected

MegAlign Pro Interface » Panels » Details panel » When one feature is selected

If a single feature has been selected in a track in the Overview or Sequences view (e.g., by clicking one time on the feature), the Details panel contains the following information: Heading Feature name (in blue). Type – Feature type. Left…

Supported file types

Appendix » Supported file types

For a list of file formats supported by this DNASTAR product, please see the File Formats page of our website.

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…

Table view

MegAlign Pro Interface » Views » Table view

To access the Table view, perform a BLAST search. When the search is complete, the Text, Table and Pairwise views are displayed together in a single popup window that is separate from the main MegAlign Pro window. To reopen all three views at a later time, click on the…

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…

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…

When a portion of a nucleotide sequence is selected

MegAlign Pro Interface » Panels » Details panel » When a portion of a nucleotide 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 …

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…

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…

See the following topics to learn how to: Move the cursor to a specific position on a sequence or alignment Search for or within a sequence using a text query Search for nucleotide or residue strings Search for disagreements between…

Options section

MegAlign Pro Interface » Panels » Tracks panel » Options section

To access settings for the track type currently selected in the Tracks panel, click on the Tracks panel expand bar entitled “Options,” or choose View > Tracks > Options. The Options section varies in appearance depending upon the selection. For discussions of each…

Export data to a file

Export » Export data to a file

Subcommands of the File > Export Data command are used to export alignments, distance matrices and phylogenetic trees, as well as aligned sequences and the consensus sequence. Unless you wish to export all sequences in the project, you must first make a…

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…

Match Bar track

Tracks » Match Bar track

To display the Match Bar track: The Match Bar track is used to show similarities and differences between the query and target sequences as calculated using the Blosum 62 substitution matrix. This track is available in the Pairwise view only after performing a pairwise…

When a non-empty document is open

MegAlign Pro Interface » Panels » Details panel » When a non-empty document is open

If a document is open and contains sequences (whether they have been aligned or not) and nothing is selected, the Details panel contains the following information: Heading The project filename. Sequence type – DNA, RNA, or…

When one sequence is selected

MegAlign Pro Interface » Panels » Details panel » When one sequence is selected

If a single sequence has been selected in any view, the Details panel may contain a subset of the following information: Heading The default name, if present, appears in blue above ‘Organism.’ Organism – The organism from which the…

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…

Create or Open a Project

Before you can add sequences to a project and align those sequences, you first need to create a MegAlign Pro project. If you already have a project from MegAlign Pro (or its predecessor, MegAlign), you can also open that to view or make changes. For details about each…

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 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…

Features

MegAlign Pro provides a wizard for copying features from one sequence to another, a procedure known as “feature mapping.” To learn more about how to map features or remove existing features, see: Map features Features, Options and Output wizard…

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…

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…

When multiple sequences are selected

MegAlign Pro Interface » Panels » Details panel » When multiple sequences are selected

If two or more sequences have been selected in any view, the Details panel contains the following information: Heading The number of sequences selected (in blue). Sequence type – DNA, RNA or Protein. Min. and Max. sequence lengths –…

Overview after other alignments

MegAlign Pro Interface » Views » Overview » Overview after other alignments

The Overview has different appearances, depending on the stage and workflow. After aligning with a method other than Mauve, or after performing a Mauve alignment that results in a single aligned block, any blocks in the Overview will be green and will have the same…

Rename sequences manually

Sequences » Rename sequences manually

To manually rename a selected sequence: Select a single sequence name from any MegAlign Pro view, then right-click on it and choose Rename Sequence(s). Alternatively, select the sequence name and choose Edit > Rename Sequence(s). The Choose Label dialog opens…

When multiple tracks are selected

MegAlign Pro Interface » Panels » Details panel » When multiple tracks are selected

If two or more tracks have been selected in the Overview or Sequences view, the Details panel contains the following information. Heading Number of tracks currently selected (in blue). Summary – Description of options available for the…

Features tracks

Tracks » Features tracks

To display sequence features: The visibility of feature (annotation) tracks in the Overview, Sequences view and Pairwise view is dependent on: Whether or not tracks are visible in those views. To display hidden tracks, click on the plus sign next to the sequence of…

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…

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…

Filter sequence search results

Search for Sequence Matches » Search for sequence matches using BLAST » Filter sequence search results

When you press the Filter results tool () in the header above the Table or Pairwise views, there are two options: Filter and Clear Filter. Clicking on the Filter option opens the following dialog: Use the drop-down menu to choose a filter type, then enter the…

Modify a multiple alignment

Perform a Multiple Sequence Alignment » Modify a multiple alignment

The following table describes ways to modify an initial multiple alignment: Task See this topic To realign a range of aligned sequences using different parameters or a different alignment engine Subalign sequences To merge two…

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…

Perform a Multiple Sequence Alignment

MegAlign Pro supports the following multiple sequence alignment methods: Clustal Omega, Clustal W, MAFFT, MUSCLE and Mauve. Click here for descriptions and a comparison of the different methods. To learn how to perform, modify, and troubleshoot multiple sequence…

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…

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…

Choosing a pairwise alignment method

Perform a Pairwise Sequence Alignment » Choosing a pairwise alignment method

MegAlign Pro has four pairwise alignment algorithms. Align to Chromosome: DNASTAR is used to perform individual pairwise alignments of 1 to 25 short sequences (typically cDNA sequences) to a chromosome-length reference sequence. This method was released with…

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…

Add ungapped sequences to a project

Sequences » Add ungapped sequences to a project

To add standard (ungapped) sequences, or additional sequences, to an existing project: You can add standard DNA, RNA or protein sequences from a wide variety of file types, including SeqNinja .star files. (See Advantages of using SeqNinja files). *Note: To add only a…

Search for text or accession number matches using Entrez

Search for Sequence Matches » Search for text or accession number matches using Entrez

The text search wizard is used to search a text query or accession number against NCBI’s Entrez databases for nucleotides or proteins. To launch the text search wizard, use one of the following commands or tools. Text Search Wizard State How To…

Gap treatment options

MegAlign Pro Interface » Views » Distance view » Gap treatment options

To change the distance metric used to generate the Distance view table, click the Change Analysis Parameters tool ( ) in the Distance view. This opens the Analysis Options dialog where you can specify the Metric and Gap Treatment. Another way to access the same dialog…

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…

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…

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…

Numeric tracks

Tracks » Numeric tracks

A numeric track displays a plot of values along one or more sequences in the project. To display numeric tracks: The visibility of numeric tracks in the Sequences view is dependent on: The origin of the project. For example, the Model ‘n’ Cα Distances…

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…

Generate a phylogenetic tree

Phylogenetic Trees » Generate a phylogenetic tree

MegAlign Pro offers four 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…

Text view

MegAlign Pro Interface » Views » Text view

To access the Text view, perform a BLAST search. When the search is complete, the Text, Table and Pairwise views are displayed together in a single popup window that is separate from the main MegAlign Pro window. To reopen all three views at a later time, click on the…

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…

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…

Search wizard: Search

Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Search

The Search screen is the second of four screens in the sequence search wizard. The Search screen is used to choose the BLAST program, as well as whether you wish to search an online database or within a locally-stored database. Choose whether you want to search…

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…

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…

Search wizard: Job

Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Job

The Job screen is the fourth of four screens in the sequence search wizard, This screen allows you to overwrite the default search name with a custom name and initiate the BLAST search. The text box contains an automatically-generated name for the search job. If…

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…

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…

Details panel

MegAlign Pro Interface » Panels » Details panel

The Details panel shows details of the application, selection or project. To open the Details panel: This panel is represented by a blue “information” icon (). If the panel is not already visible, reveal it using any of the following methods: Choose View >…

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…

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…

GC Content track

Tracks » GC Content track

To display the GC Content track: GC Content is a graph track with a scale from 0-100 showing the proportional amount of G or C residues in a sliding window of user-defined width. The visibility of GC Content tracks in the Sequences view is available only for…

Gap Fraction track

Tracks » Gap Fraction track

To display the Gap Fraction track: Gap Fraction is a graph track with a scale of 0-1 that shows the proportion of gapped positions in a sliding window centered on each position. The availability of a Gap Fraction track in the Sequences view or Pairwise view is…

Options screen

Features » Map features (copy features to another sequence) » Options screen

The Options screen is the second wizard screen of the Map Features dialog, and lets you specify mapping options. Mapping – Use the text boxes or sliders to specify percent cutoffs for: Minimum feature coverage, where: Minimum sequence…

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…

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…

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…

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…

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 …

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…

Trees section

MegAlign Pro Interface » Panels » Explorer panel » Trees section

The Trees section of the Explorer panel is used to control which phylogenetic tree is displayed in the Tree view, and allows you to create additional trees or delete them. *Note: If you are instead seeking information on the Tree section of the Style panel, click…

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…

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…

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…

Output files

Features » Map features (copy features to another sequence) » Output files

After running the Map Features step, the output consists of several files. File Name Notes PROJECT_map_features_console.txt Copy of the text that appeared for this mapping in the Console side panel in the MegAlign Pro user interface.…

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…

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 you want…

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…

Distance metric options

MegAlign Pro Interface » Views » Distance view » Distance metric options

To change the distance metric used to generate the Distance view table, click the Change Analysis Parameters tool ( ) in the Distance view. This opens the Analysis Options dialog where you can specify the Metric and Gap Treatment. Another way to access the same dialog…

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…

Part B: Perform a Mauve alignment using modified parameters

Perform a Multiple Sequence Alignment » Try it! – Perform a genomic alignment with Mauve » Part B: Perform a Mauve alignment using modified parameters

In this part of the tutorial, you will explore how to view and change parameters prior to performing a multiple sequence alignment. Choose Align > Align Using Mauve and align the sequences using the default parameters. Because this is a genomic alignment, the…

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…

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 >…

Search wizard: Query

Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Query

The Query screen is the first of four screens in the sequence search wizard. The Query screen is where you add the query sequence, i.e., the sequence for which you wish to locate matches in the NCBI BLAST database. At the top of the screen, next to “Search…

Search for Sequence Matches

This application lets you search National Center for Biotechnology Information (NCBI) databases for matches to text or sequence that you specify. You can also search for sequence matches to a local database. Query part or all of a nucleotide or protein sequence…

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…

Translation track

Tracks » Translation track

If you used MegAlign Pro’s predecessor, MegAlign, you might recall being able to toggle between displaying the alignment as a nucleotide or protein sequence. MegAlign Pro improves upon that functionality by letting you display both versions of the sequence at the…

Perform a Gene Homology Alignment

The ability to do gene homology alignments was added in Lasergene 17.6, released in early 2024. This method is for nucleotide sequences only and is set up using a simple wizard with five screens. With this method, you can perform a phylogenetic analysis of much larger…

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…

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…