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TI2BioP: Topological Indices to BioPolymers
* 1, 2 , 3 , 2, 4
1  CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208 Matosinhos, Porto, Portugal.
2  Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
3  Centro de Bioactivos Químicos, Universidad Central “Marta Abreu” de Las Villas (UCLV), Santa Clara, 54830, Cuba
4  CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal


TI2BioP (Topological Indices to BioPolymers) is a software to estimate topological indices (TIs) from two-dimensional (2D) graphical approaches for the natural biopolymers DNA, RNA and proteins The methodology mainly turns long biopolymeric sequences into 2D artificial graphs such as Cartesian and four-color maps but also reads other 2D graphs from the thermodynamic folding of DNA/RNA strings inferred from other programs. The topology of such 2D graphs is either encoded by node or adjacency matrixes for the calculation of the spectral moments as TIs. These numerical indices were used to build up alignment-free models to the functional classification of biosequences and to calculate alignment-free distances for phylogenetic purposes. We released the version 2.0 of the software that can be freely downloaded from

Keywords: 2D graphs, Topological indices, Alignment-free models, Phylogenetics
Comments on this paper
Humbert G. Díaz
TI2BioP upgrade?
Dear Dr. Agüero-Chapin

Thank you by your participation in the conference.
With respect to TI2BioP I have a couple of questions.
Are you planning an upgrade of the software or this is the definitive version?
Which ones could be the new improvements in a new upgrade?

Do you consider the possiblity of reading other types of string information like NMR signals,
EEG signals, Mass Spectra data, etc.?
Do you consider the possibility of calculation other types of numerical parameters?

Sincerely yours,
Guillermin Agüero-Chapin
Yes, TI2BioP will be upgraded soon.
We are thinking to rewrite the program in python with a new more friendly interface and new utilities that could comprise the reading/processing of new entry data (not only fasta files) will be introduced. Probably we could introduce structural data like pdb files or NMR signals for proteins
So far, our aim is just to derive topological indices, specially the spectral moments, from different sequences/graph types.

All th best, and thanks for the invitation to MOL2NET