Software productions


Research software & algorithms




The github team "Phylo42" aggregates our collaborations related to the subjects of phylogentic placement and phylo-k-mer based algorithms :

  • RAPPAS : a alignment-free approach of phylogenetic placement, for which I developped the concept of phylo-k-mer with F. Pardi.
  • XPAS : a C++ library dedicated to phylo-k-mer computation developed with N. Romashchenko, E. Rivals and F. Pardi that will become the core of all phylo-k-mer based algorithms.
  • SHERPAS : a software dedicated to genome recombination detection, with in our case a focus on Viral recombination, , develped with G Scholz, E. Rivals and F. Pardi.
  • RAPPAS 2 : a optimized / scalable implementation of RAPPAS algorithm, based on the XPAS library, develped with N. Romashchenko, E. Rivals and F. Pardi.
  • PEWO : the 1st platform for phylogenetic placement benchmarking.




  • ORTHOINSPECTOR :  a command-line and graphical software to predict orthology relatioships between hundreds of complete proteomes.  




  • ORTHOINSPECTOR : the orthoinspector database allows to query orthology prediction computed by Orthoinspector for thousands of species
  • KD4V : a database of of genetic variants involved in, that includes Knowledge Discovery and Data Mining tools. (Down in 2018)


Industrial processes


Since 2019, I'm responsible for the development of industrial processes dedicated to environmental DNA (eDNA) analysis.
This work is lead by Spygen, a private research laboratory dedicating its service and innovation to species conservation and biodiversity discovery. 
My work includes infrastructure construction, analysis pipelines, software development, web frameworks and co-development with academic and private partners.


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