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Sequences
Sequences
You can add the following types of sequences to a MegAlign Pro project: Ungapped sequences, including SeqNinja files Gapped sequences Automatic translations of nucleotide sequences Only sequences that meet filtering thresholds Multi-segment…
Subalign sequences
Perform a Multiple Sequence Alignment » Modify a multiple alignment » Subalign sequences
While sequences such as full-length calmodulin proteins typically align well throughout the entire length of the polypeptides, full-length alignments of other sequences may not generate such neat blocks of similarity. For example, multiple sequence alignments of…
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…
Unalign aligned sequences
Perform a Multiple Sequence Alignment » Unalign aligned sequences
To unalign all sequences in an alignment: Choose Align > Unalign All. When the following message appears, click OK. Execution of this command causes gaps to be removed from all of the previously aligned sequences. The sequences are then automatically…
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…
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…
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…
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…
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…
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…
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…
Layout section
MegAlign Pro Interface » Panels » Tracks panel » Layout section
To access options affecting the height of a track and the space above and/or below the track, click on the Tracks panel expand bar entitled “Layout,” or choose View > Tracks > Layout. Changes made in this section are applied to all currently selected…
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…
Favorites section
MegAlign Pro Interface » Panels » Places panel » Favorites section
The Favorites section is similar to the bookmarks folder for a web browser. It contains a list of previously-visited locations that you have decided you may wish to visit again. To access the Favorites section: Click on the Places panel expand bar entitled…
Recent section
MegAlign Pro Interface » Panels » Places panel » Recent section
When you perform a search for a gene or numerical sequence location using Edit > Go To Position, each found location is automatically stored in the Recent section. Access this section by clicking on the Places panel expand bar entitled “Recent,” or by choosing View…
Search for Sequences Online
Search for Sequences Online
This application lets you search National Center for Biotechnology Information (NCBI) databases for matches to text or sequence that you specify. Query part or all of a nucleotide or protein sequence against one of NCBI’s sequence databases using the Basic…
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…
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…
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 –…
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…
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…
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…
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.…
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…
Reverse complement one or more sequences
Sequences » Reverse complement one or more sequences
To reverse complement one or more sequences: Select one or more sequences in the Overview or Sequences view. Do either of the following: Press the Reverse Complement tool () in the toolbar. Right-click on the selection and choose Reverse…
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…
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…
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…
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.…
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…
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…
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…
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…
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 –…
Align selected unaligned sequences with an existing alignment
Perform a Multiple Sequence Alignment » Modify a multiple alignment » Align selected unaligned sequences with an existing alignment
In some cases, you may have already aligned sequences, then decide to completely realign the same sequences plus certain selected unaligned sequences. To align selected unaligned sequences with an existing alignment: Add sequences to the project and align some or…
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…
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…
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…
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.
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…
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…
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…
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.…
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…
Ruler tracks
Tracks » Ruler tracks
To display rulers: The visibility of ruler 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 interest in the…
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…
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…
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…
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.…
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. …
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…
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…
Trim an Alignment
Trim an Alignment
After performing a multiple or pairwise alignment, you may wish to trim off one or both ends before realigning, saving or exporting. To trim one or both ends from an alignment: Perform a multiple sequence alignment then use either of the methods below: Use your…
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…
Hydropathy – Kyte-Doolittle
Tracks » Biophysics tracks » Hydropathy – Kyte-Doolittle
The Hydropathy – Kyte-Doolittle track predicts regional hydropathy of proteins from their amino acid sequences, using the approach of Kyte and Doolittle, 1982. Hydropathy values are assigned for all amino acids and are then averaged over a user-defined window. The…
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…
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…
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…
Hydropathy – Hopp-Woods
Tracks » Biophysics tracks » Hydropathy – Hopp-Woods
The Hydropathy – Hopp-Woods track predicts protein antigenic determinants by searching protein sequences for the area of greatest local hydrophilicity. Hopp and Woods, 1981, make two assumptions in using hydrophilicity to find antigenic determinants: 1) antigenic…
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…
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…
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…
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…
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…
Secondary Structure – Chou-Fasman
Tracks » Biophysics tracks » Secondary Structure – Chou-Fasman
The Secondary Structure – Chou-Fasman track predicts secondary structure of proteins from the crystallographic structures of their amino acid sequences. Secondary structure prediction methods from the1970s and 1980s rely on the propensities of individual…
Hydropathy – Parker
Tracks » Biophysics tracks » Hydropathy – Parker
The Parker track uses the method of Parker et al., 1986, which is a hydrophilicity scale based on high-performance liquid chromatography retention times of model synthetic peptides. Hydrophilicity measures have been used extensively in the prediction of antigenic amino…
Stability – Aliphatic Index
Tracks » Biophysics tracks » Stability – Aliphatic Index
The Stability – Aliphatic Index track (Gasteiger et al. 2005) predicts regional stability by calculating the relative volume occupied by aliphatic side chains. This is a positive indicator of globular protein thermostability. This method is only available for…
Stability – Isoelectric Precipitate
Tracks » Biophysics tracks » Stability – Isoelectric Precipitate
The Stability – Isoelectric Precipitate track predicts regional instability by identifying uncharged regions at a given pH, which have an increased potential to aggregate if surface exposed. This method uses the pKa tables from Lehninger et al., 2005. To apply…
Antigenicity – Welling
Tracks » Immunogenicity tracks » Antigenicity – Welling
The Welling track predicts antigenicity using the method of Welling et al., 1985. Previous methods assumed that antigenic regions were mainly hydrophilic regions on the surface of a protein. By contrast, the Welling method is based on the percentage of each amino acid…
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…
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…
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…
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…
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…
Stability – Instability Index
Tracks » Biophysics tracks » Stability – Instability Index
The Stability – Instability Index track estimates the stability of the protein in a test tube. The Instability Index is calculated using the approach of Guruprasad et al., 1990,, which predicts regional instability by calculating the weighted sum of dipeptides…
Map features (copy features to another sequence)
Features » Map features (copy features to another sequence)
MegAlign Pro’s feature mapping lets you map a single annotation or all annotations from a source sequence to a target sequence. The sequences involved must have been previously aligned. During the process, you may optionally filter annotations so as to…
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…
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…
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…
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…
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…
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…
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…
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 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…
Available color schemes
MegAlign Pro Interface » Panels » Style panel » Multiple Alignment section » Available color schemes
The Multiple alignment and Pairwise alignment sections allow you to select color schemes for sequences in the Sequences and Pairwise views, respectively. Each available color scheme is described below: Color Scheme Description Nucleotide Legend…
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…
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…
MAFFT alignment options
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence alignment methods and options » MAFFT alignment options
The MAFFT algorithm is for gene level alignment of either protein or nucleotide sequences. If you want to align a large number of sequences in MegAlign Pro, we recommend using this algorithm. As of the Lasergene 17.3 release (August 2021), MegAlign Pro uses MAFFT7.…
Troubleshooting “fatal error” in Clustal Omega alignments
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Troubleshooting “fatal error” in Clustal Omega alignments
Clustal Omega requires that each sequence in an alignment contain at least one residue that is not an ambiguity code. DNA sequences must contain at least one A, C, T or G. RNA sequences must contain at least one A, C, U, or G. Protein sequences must contain at…
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…
Troubleshooting “wrong type” or “too long” errors
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Troubleshooting “wrong type” or “too long” errors
Error message that sequences are the wrong type or are too long: After beginning an alignment, an error message will appear if the sequences are not of the appropriate type or are too long for the selected algorithm. If performing a MUSCLE or Clustal Omega alignment,…
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…
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,…
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…
Consensus Match track
Tracks » Consensus Match track
To display the Consensus Match: To display or hide the Consensus Match track in the Sequences view footer, perform an alignment and then check or uncheck the Consensus Match box in the Tracks panel. This box is only visible after performing an alignment. How…
Clustal Omega alignment options
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence alignment methods and options » Clustal Omega alignment options
The Clustal Omega 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 Omega. If you wish to change method options, instead choose Align >…