Phylogenic tree reconstruction through the Kruskal algorithm

Abstract

The genetic code of an organism defines which chemical transformations may occur in its cell(s). This set of reactions is the cell’s metabolism. From the mathematical point of view, the cell’s metabolism can be described as a directed network interconnecting metabolites (molecules) through the reactions that generate one from another [1]. r1 : A_ext→ A r2 : B_ext ⇀↽ B r3 : P→ P_ext r4 : E→ E_ext r5 : A→ B r6 : A→ C r7 : A→ D r8 : B ⇀↽ C r9 : B→ P r10 : D + C→ P + E Most organisms share their hubs (water, NAD+, ATP, pyruvate, ...) and main pathways (TCA, glucolysis, pentose-phosphate, ...), since all evolved from common ancestors. Speciation is responsible for the development of new pathways and incorporation of new metabolites into the metabolism of certain species, which result in the branching of the evolutionary tree. So the analysis and comparison of different organism’s metabolisms should give hints of their distances from the evolutionary point of view. COMPARING NETWORKS