PaTre: a method for Paralogy Trees construction

Genes belonging to the same organism are called paralogs when they show a significant similarity in the sequences, even if they have a different biological function. It is an emergent biological paradigm that the families of paralogs in a genome derive from a mechanism of iterated gene duplication-with-modification. In order to investigate the evolution of organisms, it can be useful to infer the duplications that have taken place starting from an hypothetical original gene, and that have led to the current paralog genes family. This information can naturally be represented in a paralogy tree. Here we present a method, called PaTre, to generate a paralogy tree from a family of paralog genes. PaTre uses new techniques motivated by the specific application. The reliability of the inferential process is tested by means of a simulator that implements different hypotheses on the duplication-with-modification paradigm, and checked on real data.