Pairwise Alignment

Learn pairwise alignment in Geneious Prime. Use dot plots to identify repeated regions and inversions, then align DNA sequences with optimized gap penalties. Two short tutorials covering the full pairwise alignment workflow.

Course Content

Pairwise Alignment of DNA Sequences

Align two DNA sequences in Geneious Prime and get the result right. This tutorial covers algorithm selection, gap penalty tuning, mismatch highlighting, and how to handle inverted regions that standard pairwise alignment cannot resolve.
LENGTH 5 minutes

How to Use Dot Plots to Explore Pairwise Relationships

Visualize sequence similarity beyond what alignment can show. Learn to read dot plots in Geneious Prime, adjust word size and sensitivity, and identify repeated regions, inversions, and translocations in 3 minutes.
LENGTH 3 minutes

Recommended Resources

What function should I use?

The difference between Pairwise/Multiple alignment, de novo Assembly, and Map to Reference.

Which multiple alignment algorithm should I use?

Four different multiple alignment algorithms are available in Geneious Prime.

Can I call SNPs on individual sequences aligned to a reference?

Learn how to call SNPs on the pairwise alignment/assembly.

Manual for Pairwise Alignment

A guide to using pairwise alignment in Geneious.

More Geneious Academy

TUTORIALPractice Pairwise Alignment
Use this practical exercise to align pairs of DNA and protein sequences using dot plots and alignment algorithms.
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VIDEO SERIESMultiple Alignments
Watch how to perform multiple alignments and assess levels of homology among sequences before constructing a phylogeny.
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VIDEO SERIESMauve Alignment
Watch the series and learn how to use the Mauve plugin. Align genomes and convert alignments into standard alignments.
Watch Series
VIDEO SERIESWorking with GenBank
Watch the series on how to access GenBank, and prepare and submit sequences and alignments to the GenBank database.
Watch Series
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