Multiple Alignments

Use multiple alignments to assess levels of homology among a group of sequences before constructing a phylogeny.

Introduction to Multiple Alignments

Choose an alignment algorithm, perform a multiple sequence alignment using MUSCLE and view the alignment.
2 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

Practice aligning sequences, building a phylogenetic tree, and viewing and manipulating the tree.
Use a dot plot to view regions of similarity then determine homology with pairwise alignment of related sequences.
Watch the series and learn how to use the Mauve plugin. Align genomes and convert alignments into standard alignments.
Use the map to reference tool to map next-generation sequencing data against a reference, and assemble coronavirus genomes.
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