Pairwise Alignment in Geneious Prime

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

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VIDEO SERIESWorking with GenBank in Geneious Prime
Access GenBank, prepare and submit sequences and alignments to the GenBank database from the Geneious interface.
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