Compression Based Classification of Primate Endogenous Retrovirus Sequences

The highly divergent character of retrovirus sequences makes cross family alignment based classification of whole genomes difficult and unreliable. Standard methods thus focus on alignment based classification using only specific elements such as pol and env retroviral genes. In this paper a topology tree of exoand primate endogenous retrovirus sequences based on whole genomes is presented. In order to avoid the necessity of making an alignment, compression was used to approximate a mutual information based distance between sequences.