Geneious Prime

DNA Sequence Alignment

Sequence alignment, visualization, and editing. Select from multiple algorithms including ClustalO, MUSCLE, MAFFT and LASTZ.
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Sequence 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 multiple DNA alignments in one software

Select from a variety of alignment algorithms without leaving Geneious Prime. Alignments include:

  • The Geneious Aligner
  • Clustal Omega
  • MUSCLE
  • Local Re-alignment
  • Pairwise alignment
  • Translation Align
  • Consensus Align
  • MAFFT (available as a plugin)
  • MAUVE (available as a plugin)
  • LastZ (available as a 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.

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Phylogenetic Trees

Build phylogenetic trees using peer-reviewed algorithms, including RAxML and PAUP*

Assembly and Mapping

De novo assembly or reference mapping using industry leading algorithms, including TopHat and Velvet

Sanger Sequencing

Trim, assemble, and view Sanger sequencing trace files. Powerful SNP detection and variant calling.

Import Data

Import and convert common file types as well as their annotations and notes with a simple drag and drop

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