It’s no secret that there are many multiple sequence alignment tools out there, but an initial sequence alignment only gets you so far. It’s the post-alignment analysis that really moves you down the path of answering your research questions. MegAlign Pro offers everything you need for each stage of a multiple sequence alignment, not only the algorithms needed for aligning both gene-level and genome-scale sequence data, but also the capability to dig deep in the post-alignment stage.
MegAlign Pro guides you through the post-alignment process, including generating and comparing multiple phylogenetic trees, and identifying and analyzing variants across genomic strains. You can easily separate interesting regions for new subalignments, edit and trim individual sequences or the entire alignment, and customize the appearance of your alignment before generating high-quality images, suitable for publication.
Sequence alignment software features
- Align DNA, RNA, or protein sequences using Clustal Omega, Clustal W, MAFFT, MUSCLE, and Mauve multiple sequence alignment methods.
- Utilize automated guidance to choose an alignment method for your specific sequences based on quantity, length, and type.
- Identify and evaluate variants between viral, mitochondrial, or chloroplast genomes.
- Easily trim ends at the beginning or end of an alignment.
- Realign a range of aligned sequences using different parameters or a different alignment method.
- Create profile alignments by merging two existing completed alignments together.
- Generate, customize, and compare multiple phylogenetic trees using RAxML, for computer Maximum Likelihood trees, or the Neighbor Joining method.
Multiple sequence alignment in 4 simple steps
Align sequences using desired method
Generate and compare phylogenetic trees
Customize appearance and export for publication
Learn more about our Multiple Sequence Alignment Software
Resources | Tutorials | FAQs | Citations | User Guide
Please see the resources below for more information on our sequence alignment software, MegAlign Pro.
Two ways to find the best MegAlign Pro multiple sequence alignment method for your data
Watch one of our videos or check out one of our written tutorials to learn more about using our sequence alignment software, MegAlign Pro.
Aligning Genomes Using Mauve
MegAlign Pro allows you to perform multiple genome alignments using the Mauve algorithm. After alignment, create phylogenetic trees and explore sequence tracks for downstream analysis.
Merging and Realigning Sequences in MegAlign Pro
In this video, learn how to perform profile alignments to merge two alignments together. In addition, learn how to merge and realign additional sequences in your MegAlign Pro project.
Aligning Multi-Segment Files
In this video, learn how to work with multi-segment files in MegAlign Pro. Multi-segment files are files that consist of more than one chromosome, contig, or fragment, and must be aligned end to end before conducting multiple sequence alignments.
Adding Sequence Files for Alignment in MegAlign Pro
Learn how to load different nucleotide and protein sequences into MegAlign Pro for multiple and pairwise sequence alignment and phylogenetic trees. This video walks you through different ways to add and organize your sequence data prior to performing an alignment.
Supported File Types in MegAlign Pro
Learn about the different files types supported by MegAlign Pro, including FASTA files and GenBank files.
How do you create a multiple sequence alignment?
Performing a multiple sequence alignment in MegAlign Pro is easy…
Performing a multiple sequence alignment in MegAlign Pro is easy.
- From the Welcome screen, choose New Alignment.
- Select the sequences you wish to align.
MegAlign Pro will perform the alignment using the alignment method and parameters determined to be the most appropriate for your data.
- From the Welcome screen, choose New Alignment with options.
- Select the sequences you wish to align.
- Specify the alignment algorithm, change other settings as desired, then click Align to begin the alignment.
What multiple sequence alignment methods are available for DNA and protein?
MegAlign Pro includes includes Clustal Omega, Clustal W, MAFFT, and MUSCLE multiple sequence alignment methods.
Can I use MegAlign Pro to align my ABI/trace files or other sequencing reads?
The short answer is that you should not use MegAlign Pro to align ABI/trace or other raw read files, but should instead assemble the reads using SeqMan Ultra or SeqMan NGen….
The short answer is that you should not use MegAlign Pro to align ABI/trace or other raw read files, but should instead assemble the reads using SeqMan Ultra or SeqMan NGen.
The terms sequence alignment and sequence assembly mean very different things but are often used interchangeably. This can lead to confusion for many researchers. Below, we define each term and which Lasergene application to use for that workflow.
MegAlign Pro is sequence alignment software. This type of software is used to check sequence similarity or evolutionary relatedness between two or more organisms or strains. Examples of sequences that you might want to align would include a) sequences from different strains of the same virus, with the goal of seeing how the virus is mutating over time, and b) histone gene sequences from different species of plants and animals, with the goal of creating a phylogenetic tree showing their evolutionary relationships.
Common sequence types used for sequence alignment are .fasta and .genbank.
Some multiple sequence alignment software applications, including MegAlign Pro, allow you to specify a reference sequence to use in the alignment. In this case, the reference is treated as the “standard” sequence that other sequences will be compared to. Residues in other sequences can be colored/displayed/hidden to show visually which residues match (or do not match) the reference at each position.
By contrast, sequence assembly software is used to create longer consensus sequences from short fragments of a single sample of DNA, commonly known as “sequencing reads” or just “reads.”
Common sequence types used for sequence assembly include .fasta, .fas, .fastq, and .abi. Within Lasergene, SeqMan Ultra is used to assemble .abi trace data files, while SeqMan NGen is used to assemble all other file types, including sequences produced using Illumina, PacBio and Oxford Nanopore (ONT) sequencing technologies. MegAlign Pro is not used for any type of sequence assembly.
As with sequence alignment, a reference sequence can also be specified in sequence assembly. But in this situation, the reference is used as a template or scaffold, allowing DNA fragments to be assembled into larger contigs faster and more accurately than assembling them de novo.
Is a multiple genome alignment method available?
Yes. MegAlign Pro’s Mauve algorithm has high capacity and uses MUSCLE to perform block alignments of microbial genomes. This algorithm was developed in the Genome Evolution Laboratory at the University of Wisconsin-Madison.
What information is available for the variants in my genomic alignment?
After performing an assembly, MegAlign Pro can calculate variants between other sequences and the currently-specified reference sequence, or between all sequences and the consensus…
After performing an assembly, MegAlign Pro can calculate variants between other sequences and the currently-specified reference sequence, or between all sequences and the consensus.
Details about the variants in your alignment, including position, feature, impact, and translation change, can be evaluated in the Variants table, which you can access by clicking the Variants tab or by choosing View > Variants > Show.
What is a profile alignment?
Profile alignments merge two existing multiple sequence alignments without removing any of the existing gaps. However, new gaps may be automatically inserted to reconcile the new alignment.
What methods does MegAlign Pro offer for computing phylogeny?
MegAlign Pro offers two methods for generating phylogenetic trees: RAxML, for computer Maximum Likelihood trees, and the Neighbor Joining method, which uses the BIONJ algorithm.
Does MegAlign Pro support multiple phylogenetic trees in a single project?
Yes. MegAlign Pro makes it easy to to have multiple trees for a single alignment, so that you can easily compare using different phylogenetic methods or changes to the alignment.
How do I export an image of my multiple sequence alignment?
Choose File > Export Image > (View Name) and choose the export format: Adobe PDF (.pdf), Microsoft PowerPoint-optimized (.pptx), PNG image (.png) or JPG image (.jpg, .jpeg).
Can I modify my multiple sequence alignment?
Lasergene’s sequence alignment software, MegAlign Pro, supports multiple ways to modify an alignment. You can:…
Lasergene’s sequence alignment software, MegAlign Pro, supports multiple ways to modify an alignment. You can:
- Trim ends at the beginning or end of an alignment.
- Realign a range of aligned sequences using different parameters or a different alignment engine.
- Merge two existing completed alignments together.
- Add all/selected sequences from the “Unaligned Sequences” area into the current alignment, while retaining all of the gaps of the original, pre-merge alignment.
- Realign existing aligned sequences plus selected unaligned sequences
Can I modify individual sequences within my multiple sequence alignment?
Yes. MegAlign Pro gives you the ability to reverse complement, edit, and trim individual sequences within an alignment.
What’s the easiest way to find sequence matches for my consensus sequence?
MegAlign Pro’s Search wizard, accessed using Search > Sequence Search, lets you search a query sequence against one of NCBI’s BLAST databases. The sequence can be part or all of an active sequence, another sequence file on your computer, or typed/pasted-in text.
Can I map features from an annotated source sequence to a closely related sequence?
MegAlign Pro’s feature mapping (Features > Map Features) commands let you map a single annotation or all annotations from a source sequence to a target sequence. The sequences …
MegAlign Pro’s feature mapping (Features > Map Features) commands let 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 include/exclude specific gene types. Feature mapping is most commonly used to map desired annotations from a “completely annotated” sequence to a closely-related but “incompletely annotated” one.
Can I perform a MUSCLE alignment with multi-segment sequences?
Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment sequences. When you enter a group of sequences into MegAlign Pro using the …
Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment sequences. When you enter a group of sequences into MegAlign Pro using the File > Add Sequences End-to-end command instead of the standard File > Add Sequences command, the entire data set will be concatenated end-to-end and treated as a single multi-segment sequence.
What’s the best way to add gapped sequences to my multiple sequence alignment project?
To import gapped sequences from an existing MegAlign Pro file, use File > Open and choose the .msa file. Once the project is open, select all the sequences, then use Align > Unalign Selected.…
To import gapped sequences from an existing MegAlign Pro file, use File > Open and choose the .msa file. Once the project is open, select all the sequences, then use Align > Unalign Selected.
To import gapped nucleotide sequences from another type of file, use SeqMan Pro to remove the gaps. Launch SeqMan Pro, then drag and drop the gapped sequence file(s) onto the SeqMan Pro window. Select all sequences, then choose Contig > Export Sequences > Single File. Select either FastA or GenBank Flat File format and choose a file name and location. Make sure that Include gaps is left unchecked, and then click Save. The sequence(s) in the newly saved file can now be added to MegAlign Pro in the usual way.
Which multiple sequence alignment method should I use?
For gene-level alignment of either protein or nucleotide sequences, use Clustal Omega, Clustal W, or MAFFT. They offer editable options for speed, capacity, algorithm, etc., and are the only …
For gene-level alignment of either protein or nucleotide sequences, use Clustal Omega, Clustal W, or MAFFT. They offer editable options for speed, capacity, algorithm, etc., and are the only methods available for “profile” alignments. The disadvantages to gene-level aligners is that sequences must be on same strand, and that large rearrangements (e.g., inversions, translocations) are not allowed. For genome-level alignment of nucleotide sequences, use Mauve. Mauve has high capacity and uses MUSCLE to create multiple alignments for each block that contains more than a single sequence.
Rapid Detection of Novel Coronavirus (COVID19) by Reverse Transcription-Loop-Mediated Isothermal Amplification
Lamb, Laura E. and Bartolone, Sarah N. and Ward, Elijah and Chancellor, Michael B. (2/14/2020). Available at SSRN: https://ssrn.com/abstract=3539654
Point-of-care diagnostic assay for the detection of Zika virus using the recombinase polymerase amplification method
Nadina I. Vasileva Wand, Laura C. Bonney, Robert J. Watson, Victoria Graham, Roger Hewson. J Gen Virol. 2018 Aug; 99(8): 1012–1026. Published online 2018 Jun 13. doi: 10.1099/jgv.0.001083
Environmental Bacteria Involved in Manganese(II) Oxidation and Removal From Groundwater
Piazza Ainelén, Ciancio Casalini Lucila, Pacini Virginia A., Sanguinetti Graciela, Ottado Jorgelina, Gottig Natalia. Frontiers in Microbiology, Vol 10, 2019, pg 119.
Subgenotyping and genetic variability of hepatitis C virus in Palestine
Rayan Da’as S, Azzeh M (2019). PLoS ONE 14(10): e0222799.
Veillonella infantium sp. nov., an anaerobic, Gram-stain-negative coccus isolated from tongue biofilm of a Thai child
Mashima et al., Int J Syst Evol Microbiol 2018;68:1101–1106.
Genetic and phylogenetic analysis of the outer capsid protein genes of Indian isolates of bluetongue virus serotype-16
Saxena A, Biswas SK, Chand K, Naskar J, Chauhan A, Mohd G, Tewari N, Ain KU, Ramakrishnan MA, Pandey AB (2018). Veterinary World, 11(8): 1025-1029.
Identification and genetic characterization of a novel Orthobunyavirus species by a straightforward high-throughput sequencing-based approach
Shifman, O., Cohen-Gihon, I., Beth-Din, A. et al. Sci Rep 9, 3398 (2019) doi:10.1038/s41598-019-40036-4.
Molecular analysis of cox-1 and 18S rRNA gene fragments of Eimeria species isolated from endangered grouse: capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix)
Stenzel, T., Dziewulska, D., Michalczyk, M. et al. Parasitol Res (2019) 118: 461.
A Novel Alphabaculovirus from the Soybean Looper, Chrysodeixis includens, that Produces Tetrahedral Occlusion Bodies and Encodes Two Copies of he65
Harrison, R.L.; Rowley, D.L.; Popham, H.J.R. Viruses 2019, 11, 579.
Detection of Signal Regulatory Protein α in Saimiri sciureus (Squirrel Monkey) by Anti-Human Monoclonal Antibody
Souza HAS, Costa-Correa EH, Bianco-Junior C, Andrade MCR, Lima-Junior JC, Pratt-Riccio LR, Daniel-Ribeiro CT and Totino PRR (2017). Front. Immunol. 8:1814. doi: 10.3389/fimmu.2017.01814
Patatin‐like phospholipases in microbial infections with emerging roles in fatty acid metabolism and immune regulation by Apicomplexa
Wilson, S. K. and Knoll, L. J. (2018), Molecular Microbiology, 107: 34-46. doi:10.1111/mmi.13871.
The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa
Escasa SR, Harrison RL, Mowery JD, Bauchan GR, Cory JS (2019). PLoS ONE 14(2): e0209937.
Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei
Mugo E, Clayton C (2017). PLOS Pathogens 13(8): e1006560.
Serves all my needs
“This application serves to collate all my data from multiple sequences into one easy to read and manage file. This is a great program which serves all my needs and reduces the time spent performing analysis.”
“I’ve used MegAlign Pro to do multiple sequence alignments of both amino acid and nucleotide sequences. It produces beautiful graphics for inclusion in posters, etc. as well as accurate and informative alignments.”
Gained great insight
“We have used MegAlign to help identify short conserved motifs in orthologous genes with very low shared sequence similarity, and have gained great insight from these results.”
Quick and easy
“Quick and easy multiple alignments, The drag and drop ability makes alignments fast to assemble.”
“Most comprehensive and full-feature alignment software I have found.”