A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny.The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.Past events that gave birth to biological entities can be tentatively reconstructed based on collections of descriptors traced in ancient or present-day creatures. Using genomic sequences, an estimate of the relative time separating branching events, previously supported by geological records, could be formalized using mathematical models. The use of proteins for evolutionary reconstructions was vastly explored as soon as the first amino acid sequences were made available [1-9]. The rich biological information contained in protein sequences stems from their being, on the one hand, translation of genes that reflect the history of genetic events to which the species has been subjected, and on the other hand, effectors of the functions co