Methods

First an Archaea Gene was selected to be used to find homologous proteins through BLAST. The Archaea chosen in the case was Methanocaldococcus jannaschii's bifunctional short chain isoprenyl diphosphate synthase (AAB98865). A protein Blast was preformed ignoring model proteins and uncultured proteins to get a varied set of species with well characterized homologous proteins. The Coding Nucleotide Sequence was found for each of these genes and added into MEGA a phylogenetic Tree analysis software. After collecting a large enough sample size of archaea, bacterial and eukaryotic homologous proteins, these were aligned using MUSCLE (Multiple Sequence Comparison by Log-Expectation). Once aligned the proteins were then analyzed to find the optimal model for generating a phylogenetic tree. In this case it was General Time Reversible model with a Gamma distribution with 5 Gamma Categories. This was then used in a Maximum Likelihood statistical method to generate a phylogenetic tree.

Once the Tree was generated it was necessary to find a proposed root of the tree which in this case required finding an outgroup as maximum likelihood does not find a root. By looking at figure 3 it was decided that the Eukaryotes and Archaea where significantly removed and were classified as the outgroup leading to the selection of a root between the archaeal branch and the others. From here the Maximum Likelihood method combined with the phylogenetic tree allowed for the prediction of a genetic sequence based on propagating the nucleotide sequence of close relatives back.