Research group BIO-GEOMAP

Our research group develops and improves methods of phylogenetic reconstruction based on mathematical tools, especially algebraic, semi-algebraic and geometrical tools. This involves studying molecular substitution models from a mathematical point of view to guarantee parameter identifiability and to provide model selection tools (including both the evolutionary model and the tree or network selection). Our research lies at the borders of phylogenetic reconstruction, algebraic statistics, algebraic geometry and computational algebra.

We are part of the larger research group INTERGAP: Interactions of Geometry and Algebra with Applications.

Senior members:

Marta Casanellas

Jesús Fernández-Sánchez

Senior Postdocs:

Roser Homs

Marina Garrote-López

Jordi Roca-Lacostena

Previous members (BSc or MSc project, PhD students or postdocs)

Angelica Torres

Mateusz Michalek

Alessandro Oneto

Anna Magdalena Kedzierska

MSc Thesis: Davinia Mañez, Eli Giralt, Esther Ibáñez, Marc Sabaté-Vidales, Joan Carles Pons, Gustavo Cilleruelo

BSc Thesis: Martí Cortada, Adrià Diéguez, Aïda Cunill, Laura Cifuentes Fontanals, Raúl Pérez Gonzalo, Alba Puy

Software developed:

• GenPhylo (by M. Cortada Garcia and A. Diéguez Moscardó): Generating heterogeneous data on gene trees as Python code; also as a Python package here
• ASAQ (by M. Garrote): algebraic and semi-algebraic phylogenetic reconstruction for quartets
• SAQ (by M. Garrote): semi-algebraic phylogenetic reconstruction for quartets
• Erik+2 (by M. Casanellas and J.Fernández): software for quartet topology reconstruction via invariants.
• SPIn (by A. Kezdierska) software for model selection of evolutionary models via invariants.
• GenNon-h (by A. Kedzierska): software for generating sequences evolving under a (discrete-time) Markov process on a tree with given branch lengths.
• EMPar (by A. Kedzierska) EM for parameter estimation of Markov models on trees