Some open source code I have contributed to:
- reconstruction of ancestral RNA structures using Small Parsimony: https://github.com/bmarchand/rna_small_parsimony. Associated publication: here.
- Implementation of Tamaki’s algorithm for directed pathwidth: https://github.com/bmarchand/rna_small_parsimony. Associated publication: here
- Selecting a maximum number of edges under a treewidth budget: https://gitlab.inria.fr/amibio/tree-diet. Associated publication: here
- A general framework for encoding and solving problems with dynamic programming over tree decompositions: https://gitlab.inria.fr/amibio/Infrared. Associated publication: here
- A simple numpy-based quantum circuit simulator: https://github.com/myQLM/myqlm-simulators