Wilke:Molecular Evolution

The Basics

Evolutionary rate (dN/dS) analyses involve a basic pipeline: sequence alignment, phylogenetic inference, and finally evolutionary rate inference. When dealing with protein coding sequences, always align using amino acid data in order to preserve codons. Then, back-translate into nucleotide data, as is required for the final step in the pipeline. Phylogenies may be made either with amino acid or nucleotide data, although an amino acid tree may be slightly more accurate.

Additionally note that a minimum of 10 sequences are recommended to achieve well-supported results in an evolutionary rates analysis.

Sequence Alignment

Commonly aligners include mafft, muscle, and prank. While prank is probably the most accurate, it is also very time consuming. We recommend using mafft for sequence alignments.

To align sequences in mafft, we additionally recommend using the "--auto" option. This will allow mafft to select the optimal alignment algorithm to use on your data.