• Software
    • DNASTAR LASERGENE
      Comprehensive Sequence Analysis
      • Lasergene Molecular Biology
      • Lasergene Genomics
      • Lasergene Protein
    • NOVA APPLICATIONS
      Protein Modeling
      • NovaFold
      • NovaFold Antibody
      • NovaDock
  • Workflows
    • Molecular Biology Workflows
      • Automated Virtual Cloning
      • Clone Sequence Verification
      • Gel Electrophoresis Simulation
      • Multiple Sequence Alignment
      • Pairwise Sequence Alignment
      • PCR Site-Directed Mutagenesis
      • PCR Primer Design
      • Phylogenetic Analysis
      • Plasmid Maps
      • Sanger Sequence Assembly
      • Sequence Editing and Annotation
  • Protein Analysis
    • Antibody Modeling
    • Epitope Prediction
    • Protein Docking
    • Protein Sequence Analysis
    • Protein Stability Prediction
    • Protein Structural Alignment
    • Protein Structure Analysis
    • Protein Structure Prediction
  • Genomics
    • Clinical Research
    • De Novo Genome Assembly
    • Mauve Genome Alignment
    • Metagenomic Assembly
    • Variant Analysis
    • Whole Genome/Whole Exome
  • Transcriptomics
    • ChIP-Seq Data Analysis
    • De Novo Transcriptome Assembly
    • RNA-Seq Alignment
  • Services
    • Protein Services
    • Genomic Services
  • Pricing
    • Academic Pricing
    • Commercial Pricing
    • Lasergene Student Licenses
    • Request a Quote
  • Resources
    • COVID-19
    • Product Updates
    • Product Notifications
    • Blog
    • Educational Software Request
    • Events
    • Documentation
    • Grant Assistance
    • Technical Requirements
      • File Formats
      • Licensing Options
  • Training
    • Help + Tutorials
    • Webinars
    • Video Library Archives
    • Technical Support Request
  • About
    • Careers
    • Distributors
    • Legal Information
    • Privacy Policy
  • Contact
  • Languages
    • English
    • العربية
    • 日本語
    • 한국어
    • 简体中文
    • Deutsch
    • Español
    • Francais
    • Português – Portugal
    • Português – Brasil
  • LANGUAGE
    • English
    • العربية
    • 日本語
    • 한국어
    • 简体中文
    • Deutsch
    • Español
    • Francais
    • Português – Portugal
    • Português – Brasil

QUESTIONS? CALL 866.511.5090

DOWNLOAD FREE TRIAL
SHOPPING CART
MY ACCOUNT
DNASTAR DNASTAR
  • Software
    • DNASTAR LASERGENE
      Comprehensive Sequence Analysis
      • Lasergene Molecular Biology
      • Lasergene Genomics
      • Lasergene Protein
    • NOVA APPLICATIONS
      Protein Modeling
      • NovaFold
      • NovaFold Antibody
      • NovaDock
  • Workflows
    • Molecular Biology
      • Automated Virtual Cloning
      • Clone Sequence Verification
      • Gel Electrophoresis Simulation
      • Multiple Sequence Alignment
      • Pairwise Sequence Alignment
      • PCR Site-Directed Mutagenesis
      • PCR Primer Design
      • Phylogenetic Analysis
      • Plasmid Maps
      • Sanger Sequence Assembly
      • Sequence Editing and Annotation
    • Protein Analysis
      • Antibody Modeling
      • Epitope Prediction
      • Protein Docking
      • Protein Sequence Analysis
      • Protein Stability Prediction
      • Protein Structural Alignment
      • Protein Structure Analysis
      • Protein Structure Prediction
    • Genomics
      • Clinical Research
      • De Novo Genome Assembly
      • Mauve Genome Alignment
      • Metagenomic Assembly
      • Variant Analysis
      • Whole Exome/Genome Sequencing
    • Transcriptomics
      • ChIP-Seq Data Analysis
      • De Novo Transcriptome Assembly
      • RNA-Seq Alignment and Analysis
  • Services
    • Protein Services
    • Genomic Services
  • Pricing
    • Academic Pricing
    • Commercial Pricing
    • Lasergene Student Licenses
    • Request a Quote
  • Resources
    • COVID-19
    • Product Updates
    • Product Notifications
    • Blog
    • Educational Software Request
    • Events
    • Documentation
    • Grant Assistance
    • Technical Requirements
      • File Formats
      • Licensing Options
  • Training
    • Help + Tutorials
    • Webinars
    • Video Library Archives
    • Technical Support Request
  • About
    • Careers
    • Distributors
    • Legal Information
    • Privacy Policy
  • Contact

MULTIPLE SEQUENCE ALIGNMENT

Perform accurate multiple sequence alignments of DNA, RNA, and protein sequences for both gene-level and genome-scale sequence data, then analyze in-depth. PRICING DOWNLOAD FREE TRIAL

Use MegAlign Pro for accurate multiple sequence alignment and in-depth analysis.

It’s no secret that there are lots of multiple sequence alignment tools out there, but we all know that an initial sequence alignment only gets you so far. It’s really the post-alignment analysis that moves us down the path of answering the questions we are asking. 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 —MUSCLE, MAFFT, Clustal W, Clustal Omega, and Mauve — but also the capability to dig deep in the post-alignment stage. MegAlign Pro performs DNA, RNA, and protein sequence alignments quickly and easily, then guides you through the post-alignment process, including generating and comparing multiple phylogenetic trees using RAxML for Maximum Likelihood trees, or the Neighbor Joining method. 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.

Multiple sequence alignment in 4 simple steps

Multiple Alignment Step 1

Step 1

Add sequences

Multiple Alignment Step 2

Step 2

Align using desired alignment method

Multiple Alignment Step 3

Step 3

Generate and compare phylogenetic trees

Multiple Alignment Step 4

Step 4

Customize appearance and export for publication

computer

Learn more about Multiple Sequence Alignment

Resources | Tutorials | FAQs | Citations | User Guide

Pricing
DOWNLOAD FREE TRIAL

Resources

Please see our resources below for more information on multiple sequence alignment.

Video Icon

Mastering Phylogenetic Tree Creation & Optimization with MegAlign Pro

Watch Webinar

Webinar Icon

Two ways to find the best MegAlign Pro multiple sequence alignment method for your data

Read Blog Post

Webinar Icon

How to Create the Best Phylogenetic Tree for Your Data Using MegAlign Pro

Read Blog Post

Video Icon

Best Practices for Sequence Alignment in MegAlign Pro Webinar

Watch Webinar

Webinar Icon

Answers to Your MegAlign Pro Webinar Questions

Read Blog Post

Webinar Icon

Tree Viewer Software

Read Blog Post

Video Icon

Aligning and Annotating Multiple Genomes Webinar

Watch Webinar

Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about using MegAlign Pro for multiple sequence alignment.

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.

FAQs

What multiple sequence alignment methods are available for DNA and protein?

MegAlign Pro’s multiple sequence alignment tools for DNA and protein include Clustal Omega, Clustal W, MAFFT, and MUSCLE.

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 is a profile alignment?

Profile alignments merge two existing multiple 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 multiple 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 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 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 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 alignment method should I use for my multiple sequence alignment?

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.

Citations

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.

computer Ready to learn more? PRICING DOWNLOAD FREE TRIAL
  • 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.”

    Ben Arnold, Immunosolv Ltd

    

  • Beautiful graphics

    “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.”

    Cynthia LeVesque, Citrus Research Board

  • 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.”

    John Allingham, Oregon State University

  • Quick and easy

    “Quick and easy multiple alignments, The drag and drop ability makes alignments fast to assemble.”

    Matthew Nilles, University of North Dakota

    

  • Comprehensive

    “Most comprehensive and full-feature alignment software I have found.”

    Gordon Wolfe, California State University Chico

Questions?

Our team of scientists is here to help!

CONTACT US

Or call (866) 511-5090

Scientists
Would you like to receive technical tips and special offers straight to your inbox? YES, SIGN ME UP!
  • Pricing
  • Software
  • Workflows
  • Resources
  • Training
  • About

Get a 14-Day free trial of our complete Lasergene package. Try before you buy!

FREE TRIAL DOWNLOAD

© 2021 — DNASTAR Privacy Policy

This website uses cookies to improve user experience and understand our web usage. By continuing to use our website, you consent to our use of cookies. Accept
Privacy & Cookies Policy
Necessary
Always Enabled