Séquence / assemblage de génome
| Tool | Description | Publication | Research unit |
| NanoBAC | Assembly of ONT reads obtained from the sequencing of BACs containing repetitive regions (such as ribosomal DNA) | UMR 1332 BFP |
Annotation
| Tool | Description | Publication | Research unit |
| EuGene | Annotation pipeline | DOI | UMR 0441 LIPME |
| IngenAnnot | Inspection of Gene Annotation | DOI | UR 1290 BIOGER |
| TEGRiP | Transposable Elements Genes RelationshIps Pipeline | DOI | UMR 1332 BFP |
| GeneNeighborhood | Analyze the orientation and distances of neighboring genes for your favorite gene set | UMR 1332 BFP |
Visualisation & Intégration de données
| Tool | Description | Publication | Research unit |
| myGenomeBrowser | Build and share your own genome browsers | DOI | UMR 0441 LIPME |
| karyoplot | Draw simple karyoplot/ideogram | UR 1290 BIOGER | |
| AskOmics | Data integration and visual query interface | UMR 1349 IGEPP |
Transcriptomique
| Tool | Description | Publication | Research unit |
| AskoR | RNAseq data analysis tool | UMR 1349 IGEPP | |
| SATQPCR | Statistical Analysis Tool for Quantitative Real-time PCR Data | DOI | UMR 1355 ISA |
Génomique comparative & métagénomique
| Tool | Description | Publication | Research unit |
| Family Companion | Compare proteomes | DOI | UMR 0441 LIPME, UMR1345 IRHS, UMR 1355 ISA |
| Alienness | Rapid detection of candidate horizontal gene transfers across the tree of life | DOI | UMR 1355 ISA / UMR 0441 LIPME |
| — | — | — | — |
| KI-S | A rapid and simple method for assessing and representing genome sequence relatedness | DOI | UMR1345 IRHS |
| SkIf | Specific k-mers Identification | DOI | UMR1345 IRHS |
| CIRM-CFBP Galaxy instance | Bacteria, comparative genomics | UMR1345 IRHS | |
| — | — | — | — |
| vitiVir | Identification and discovery of grapevine associated phytoviruses and mycoviruses | UMR 1332 BFP | |
| virAnnot | Viral Diversity Estimation and OTU Assignation for Virome Sequencing Data | DOI | UMR 1332 BFP |