• 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

• Mathematica Notebook: Computation through smooth dynamics: simulating TKFT’s (by I. Ramos)

Topological Kleene Field Theories (TKFTs) represent a new framework in the world of computational theory, where computations are introduced as flows in cobordisms. This project translates this abstract construction intro concrete terms, explicitly computing the smooth dynamics that simulate different Turing machines.