ISTREE - Informational Spectrum-based Phylogenetic Analysis

New approach in phylogenetic analysis allows at first time the assessment of functional viral evolution.

The Informational spectrum method (ISM) is based on the assumption that the protein-protein interaction encompasses two basic steps:
  • recognition and targeting between interacting proteins (long-range interactions at distances >100Å)
  • chemical binding (short range interactions at distances <5Å)
The long-range properties of biological molecules are determined by the electron-ion interaction potential (EIIP) representing the main energy term of valence electrons.

All of standard evolutionary models are based on the multiple sequence alignment (MSA). The main weakness of phylogenetic analyses based on MSA, is that sequence similarity does not necessarily imply similarity in functions. For example, two protein sequences that differ by a single mutation that is lethal for the biological function will nevertheless phylogenetically group together, whereas two proteins that differ in several mutations that do not affect biological functions will be phylogenetically separated.

In order to overcome this obstacle and to improve functional sequence analysis, we use a new distance measure based on the IS method. The ISM distance is sensitive to the position of mutation and the type of the substituted residue, in opposition to standard distances. ISM approach for generating phylogenetic trees and phylogenetic analysis (ISTREE) is not based on MSAs.

For more information of ISTREE, mathematical background, definition, properties of ISM distance and applications, please see:
  • Perovic et al. Novel phylogenetic algorithm to monitor human tropism in Egyptian H5N1-HPAIV reveals evolution toward efficient human-to-human transmission. PLoS One. 2013. 26;8(4):e61572.    Full Text

  • Perovic. Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses. J Math Chem. 2013. 51(8):2238-55.    Link

You are welcome to use our free web service ISTREE for building the informational spectrum-based phylogenetic tree. Just input the protein sequences in FASTA format and submit data.