Creating SNPtrees

In epidemiological studies, isolates usually have very little diversity and require full genomic analysis to differentiate and classify. Reducing a whole genome alignment to just the subset of statistically validated variant sequence positions provides a condensed dataset for phylogenetic analysis and classification of isolates.

Geneious Prime allows you to easily generate a whole-genome alignment suitable for generating phylogenetic trees based on single nucleotide polymorphism information (SNPtrees).

This application note provides an overview of how to generate a SNPtree in Geneious Prime, using next-generation sequencing (NGS) data from Ebola virus isolates generated by the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) during the 2014 West African Ebola outbreak.