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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…
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…
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…
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: 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…
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…
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 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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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 …
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 …
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 …
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…
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,…
Add translations of nucleotide sequences to a project
Sequences » Add translations of nucleotide sequences to a project
In MegAlign Pro 17.6 and later, you can add nucleotide sequences to an existing project as translated amino acid sequences. This functionality can be useful when you have DNA and protein sequences that you want to align together. MegAlign Pro does not support 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…
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 –…
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…
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…
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! – 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…
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…
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…
Reroot a tree
Phylogenetic Trees » Reroot a tree
Each tree in the Tree view displays an incoming root edge, which is intended to represent the location of a possible common ancestor. The root edge appears on the left of a tree drawn in the default orientation. For purposes of visualization or publication, you…
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. …
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…
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…
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…
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…
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…
Search for or within a sequence using a text query
Search » Search for or within a sequence using a text query
MegAlign Pro supports searching for sequences by their name or by any text stored as part of the sequence (e.g., the description or the name of a feature). By default, the search tools are hidden. To display them, click on the Search tool () in the upper right of…
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…
Create or Open a Project
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…
Perform a Multiple Sequence Alignment
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…
Perform a Pairwise Sequence Alignment
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…
Remove sequences from a project
Sequences » Remove sequences from a project
The following procedure causes the selected sequences to be completely removed from the project, not simply moved to the “Unaligned Sequences” area. To remove sequences from the project: Select one or more of the aligned or unaligned sequences in the Overview…
Edit gaps in a sequence
Sequences » Edit gaps in a sequence
With the release of MegAlign Pro 17.6 in 2024, you can insert, delete, or shuffle gaps in a sequence that is part of any multiple sequence alignment except a Mauve alignment. To edit gaps: Perform a multiple sequence alignment. Click View > Style > Multiple…
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…
Import a Newick-format tree
Phylogenetic Trees » Import a Newick-format tree
MegAlign Pro can open Newick trees with .newick, .txt or .tree extensions. To import a Newick-format tree file: Make any MegAlign Pro project tab active, or open a new, blank project. Trees cannot be opened from within the Welcome screen Choose File > Add…
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 a Gene Homology Alignment
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…
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…
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…
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…
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…
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…
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.…
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…
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…
Try It! – Use Local pairwise alignment to find a gene within a genome
Perform a Pairwise Sequence 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,…
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…
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…
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…
Try it! – Perform a Clustal Omega alignment
Perform a Multiple Sequence 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…
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.…
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…
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…
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…
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 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…
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…
Try it! – Perform a genomic alignment with Mauve
Perform a Multiple Sequence Alignment » Try it! – Perform a genomic alignment with Mauve
In this tutorial, you will be adding six nucleotide sequences to MegAlign Pro using drag & drop, and then aligning them with the Progressive Mauve algorithm. Drag and drop is a feature available in all Lasergene applications, and is useful for entering multiple…
When no document, or a blank document, is open
MegAlign Pro Interface » Panels » Details panel » When no document, or a blank document, is open
When no document or only a blank document (one containing no sequences) is open, the Details panel displays links to help you get started in MegAlign Pro. Heading One or more links are available. The first three options are available for blank…
Part A: Compare results from three multiple alignment methods
Perform a Pairwise Sequence Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments » Part A: Compare results from three multiple alignment methods
This part of the tutorial demonstrates that if you don’t have annotations to rely on for validating multiple alignments, a pairwise alignment is a good alternative. This tutorial uses a default MUSCLE alignment of the Drosophila melanogaster ADH gene and the…
Add sequences from a saved project to an active project
Sequences » Add sequences from a saved project to an active project
To add sequences from a saved project to an active project: Choose File > Add Sequences and select a MegAlign Pro project file (.msa). All sequences in the .msa file will be added to the “Unaligned Sequences” area of the active project.
Try it! – Perform a MUSCLE alignment with multi-segment sequences
Perform a Multiple Sequence Alignment » Try it! – Perform a MUSCLE alignment with multi-segment sequences
Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment files. Suppose you want to string together the consensus sequences from all the contigs in an assembly, or chromosomes in a genome, or exons in a gene, etc. If you enter…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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 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…
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…
Manually specify sequence type
Sequences » Manually specify sequence type
When you add a sequence to a project, MegAlign Pro uses clues in the sequence file to ascertain whether it is DNA, RNA or protein. When uncertain, it will prompt you to supply the missing information as you add the sequences. If MegAlign Pro guesses incorrectly…
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…
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…
Visually Compare Other Sequences to One Sequence
Visually Compare Other Sequences to One Sequence
You can visually compare sequences in the alignment to one of the aligned sequences by using settings in MegAlign Pro’s Style panel to highlight differences or matches. By default, the comparison is against the reference sequence, if you have specified one.…
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…
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…
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…
Consensus track
Tracks » Consensus track
To display the consensus: After any type of alignment, a consensus sequence is automatically displayed in the Sequences view header. To display or hide this consensus sequence, check or uncheck the Consensus box in the Tracks panel. This box is only visible after…
Features panel
MegAlign Pro Interface » Panels » Features panel
The Features panel lets you specify which feature types should be visible in the Overview and the Sequences view once a sequence has been expanded. To open the Features panel: Click on the Features tab (). If the panel is not already visible, reveal it using any of…