Multiple Sequence Alignment

Benchling’s multiple sequence alignment tool allows you to compare and analyze hundreds of amino acid and DNA sequences at once, and then easily share the results with your colleagues.
Media Image

From alignment to discovery in one platform

  • Compare at Scale Icon

    Compare at scale


    Quickly align and analyze hundreds of amino acid or DNA sequences to uncover similarities, differences, and key insights.

  • Collaborate Easily Icon

    Collaborate with ease 


    Share alignment results directly with colleagues so everyone can review and interpret the data together.

  • All in Benchling Icon

    All in Benchling

    Run multiple sequence alignments within the same platform you use for the rest of your research, keeping everything connected and organized.

Product Double Helix

Align, analyze, and edit sequences — all in Benchling

Compare and analyze

Centralize your alignment and analysis 

Benchling’s sequence alignment is unified with other molecular biology tools, so you can do everything in one place.

  • Align sequences alongside the rest of your molecular biology work

  • Visualize and analyze results directly on the same platform

  • Edit sequences without switching tools or losing context

Compare and Analyze - Alignments Product Image
Batch alignments

Scale with ease using batch sequence alignments 

Batch hundreds of DNA, amino acid, or protein sequence alignments, unified within Benchling’s molecular biology suite.

  • Compare hundreds of DNA, amino acid, or protein sequences

  • Run alignment in batches for faster analysis 

  • Work seamlessly within the same platform for design, editing and analysis

Batch Alignments - Alignments Product Image
Collaborate efficiently

Share and collaborate on alignments

No more digging through folders or emails. Keep your alignments organized and accessible by sharing them directly in Benchling.

  • Eliminate version confusion from local files or scattered email attachments

  • Send colleagues a direct link to any alignment in Benchling

  • Give collaborators instant access to related sequence files for added context

Collaborate Efficiently - Alignments Product Image
Pairwise (Midnight Blue) Logo
We can look at a plant and simultaneously know not only the plasmid we used, but its exact sequence and dozens of aspects about it. This takes us from using Benchling as a plant inventory system to a fully integrated biotechnology pipeline.
Nathaniel Graham

Molecular Biology Scientist, Pairwise

Powering breakthroughs for over 1,300 biotechnology companies

Helix Image