Software productions

 

Research software & algorithms

 

Phylogenetics

 

The github team "Phylo42" aggregates our collaborations related to the subjects of phylogentic placement and phylo-k-mer based algorithms :
https://github.com/phylo42

  • 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.

 

Orthology 

 

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

 

Database

 

  • ORTHOINSPECTOR : the orthoinspector database allows to query orthology prediction computed by Orthoinspector for thousands of species https://lbgi.fr/orthoinspectorv3/
  • KD4V : a database of of genetic variants involved in, that includes Knowledge Discovery and Data Mining tools. http://decrypthon.igbmc.fr/kd4v (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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