Whole genome phylogeny is important because phylogenetic analyses based on a single gene may be misleading because of a lack of informative sites or because of horizontal transfer. Our approach to whole genome phylogeny takes advantage of an information theoretical concept called mutual algorithmic information. This makes the method well suited for whole genomes where traditional alignments may not be feasible. Experiments involving mitochondrial and chloroplast genomes have produced trees congruent with currently accepted evolutionary relationships.
Phylogenetic analyses involving large numbers of taxa allow a better understanding of biodiversity.
However, commonly used phylogenetic methods such as heuristic maximum parsimony and maximum likelihood often miss the optimal tree when used in large analyses. This is because the number of possible trees increases exponentially with the number of taxa, so in practice maximum likelihood and maximum parsimony only consider a small number of possible trees. Gene finding programs are essential for analyzing existing and future DNA sequence data. If, in a nucleotide alignment, a pair of ORFs can be found in which the conceptual translated products are more conserved than would be expected from the amount of conservation at the nucleotide level, this is evolutionary evidence that the DNA sequences are protein coding. Regions found by this method are used to generate traditional dicodon frequencies for further analysis.