Explore projects

This repository includes a compressed archive with supplementary files generated for the Thesis written in partial fulfillment of the requirements for the Master of Science (OEP-Biology).

This is a fork with the necessary tools to generate reference FASTA files on the protein and gene levels and a modified orthology table, all of which are compatible with and necessary to annotate orthologs with Orthograph v0.6.3. Created to fix incompatibility issues between the information stored in the catalog from OrthoDB v10.1 and the protein ID's in the sequence headers from the RefSeq files from NCBI.

The OpenAPI Model for ASV data in AMMOD

This is a fork that only includes the script to choose the optimal annotated transcriptome after gene orthology inference with Orthograph.

ortho-overlap.py is being updated to work with the results from BUSCO as well.

Filtering a multiple sequence alignment excluding positions where a taxa group is the only representative.

A template to structure data, code and documentation for a project on the HPC-Cluster

Endpoint for getting ASV taxonomy tables as BIOM JSON files. http://gensoft.pasteur.fr/docs/biom-format/2.1.5/index.html