Analysing Consensus Sequences

You should now have produced consensus sequences for all 9 of the samples. These sequences can be aligned so that they can be used for population genetic or phylogenetic analyses. Select all the consensus sequences and click Align/Assemble→Multiple Align. Use the Geneious Aligner with the default settings.

Open the alignment and click on the Distances tab to get an overview of the nucleotide diversity within and between species. As you would expect, sequences are more similar within species than between species. In fact the sequences from A. arundinaceus (aru) are identical. You could now use the Tree building tools within Geneious Prime to conduct a phylogenetic analysis of the sequences, or for more advanced population genetic analyses, the alignment can be exported in Fasta or Nexus format for analysis in a program such as DNAsp.

This concludes the Advanced Chromatograms Tutorial