DNA and protein sequence alignment

Align sequences without juggling files. Click the Alignment button then simply switch between alignment algorithms.

Awesome alignment visualization and editing

  • Show annotations on the alignment and edit at the same time
  • Drag to remove or insert gaps
  • Join sequences together
  • Strip columns
  • Type directly into an alignment
  • Correct bad calls
  • Viewing and coloring by translation alongside allows you to correct coding sequences
  • View phylogeny alongside the alignment and link back to a tree
  • Similarity and sequence logo graphs
  • Real-time updates to the statistics panel (real-time) update according to selection
  • Spot disagreements easily with highlighting

Access a variety of alignments including ClustalW, MUSCLE and MAFFT from within one framework

Save time and stop jumping around from program to program. Select a specific task to perform without leaving Geneious. Built in alignments include:

  • The Geneious Aligner
  • ClustalW
  • Local Re-alignment
  • Pairwise alignment
  • Translation Align
  • Consensus Align
  • MAFFT- available as a plugin
  • MAUVE- available as a plugin
  • LastZ – available as plugin

Your data your way

No matter what alignment you choose, the data is still yours to edit and annotate in a way that works for you.

Better genome alignments are just a few clicks away.


Download a free trial and one of our tutorials to get to grips with the functionality of Geneious interactively.

Tutorial – Aligning Bacterial Genomes with Mauve

Learn how to align bacterial genomes using the Mauve plugin for Geneious. This tutorial covers alignment of complete genomes and ordering of draft genomes against a reference.

Tutorial – Pairwise Alignment

Develop the skills needed to align pairs of DNA and protein sequences with Geneious using dotplots and alignment algorithms.

Geneious is paramount in my research so I can’t be without it for too long.
Bob LitermanIowa State University