UMR DIADE

DIversity - Adaptation - plant DEvelopment

The DIADE Research Unit aims to understand the diversification of tropical plants, one of the main original reservoirs of biodiversity, and for which conservation, management and exploitation are an important issue for Sustainable Development.

The nine teams forming the Unit belong to IRD, University of Montpellier, CIRAD, and CNRS.

CERES Team

DYNADIV Team

PANEEC Team

EVOGEC Team

ADvENS Team

AgroLD

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1 to 10 of 49 Results

rice data Jul 31, 2026 - GraNPA true data Carrette, Camille; Muller, Cédric, 2026, "rice data", https://doi.org/10.23708/M2U8UV, DataSuds, V1, UNF:6:s2YUeS/27WhTMw1SDfr03g== [fileUNF] This dataset cointains all the output from GraNPA original paper for rice
cattle data Jul 31, 2026 - GraNPA true data Carrette, Camille, 2026, "cattle data", https://doi.org/10.23708/2G2DFB, DataSuds, V1 Cattle Pangenome variation graph data used in the GranPA paper
Supplementary command lines for the GraNPA paper Jul 30, 2026 - GraNPA other codes used for the manuscript Carrette, Camille; Muller, Cédric, 2026, "Supplementary command lines for the GraNPA paper", https://doi.org/10.23708/AU5ALD, DataSuds, V1 This file contains all the commands used for generate data and results in the GranPA paper
GranPa source code, v1 Jul 30, 2026 - GranPa Source Code Carrette, Camille; Muller, Cédric, 2026, "GranPa source code, v1", https://doi.org/10.23708/JG96WP, DataSuds, V1 This code is the version used in the GranPa paper
SAGHAS - Sowing AGrobiodiversity to HArvest Sustainability: a multi-source database of crop species cultivated for human food Jul 9, 2026 - DYNADIV Team Davy, Martin; Barnaud, Adeline; Berthouly-Salazar, Cecile; Renard Delphine; Thuillet, Anne-Celine, 2026, "SAGHAS - Sowing AGrobiodiversity to HArvest Sustainability: a multi-source database of crop species cultivated for human food", https://doi.org/10.23708/LK5VUI, DataSuds, V1, UNF:6:mNCUB06Fnpj7NbK+SblAGA== [fileUNF] Across the vast diversity of vascular plants on Earth, around 6,000 species have been used as food sources for humans. Yet, only nine crops provide more than 60% of the calories consumed worldwide. In the face of accelerating climate change, biodiversity loss, and malnutrition, t...
Supporting data and scripts produced by the GraTools software Mar 10, 2026 - gratools Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Supporting data and scripts produced by the GraTools software", https://doi.org/10.23708/M24LJG, DataSuds, V1 Here, we introduce GraTools (https://forge.ird.fr/diade/gratools), a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file. After a one-time graph import, GraTools enables rapid subgraph extraction, fasta sequence retrieval, and comprehensive...
Data used in the gratools paper Mar 6, 2026 - gratools Sabot, Francois, 2026, "Data used in the gratools paper", https://doi.org/10.23708/SOTLQU, DataSuds, V1 These are the data (mostly Pangenome variation graphs) that were used in the gratools paper only. The file is the Zenodo DOI link for the thre graphs.
Code source for GraTools v1.1.0 Mar 6, 2026 - gratools Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Code source for GraTools v1.1.0", https://doi.org/10.23708/DXOP8N, DataSuds, V1 This code is the original source code submitted for GraTools in March 2026. This is a dump of the IRD Forge git, master branch
Data used for the analysis described in GrAnnoT paper Oct 29, 2025 - GrAnnoT data and output Marthe, Nina; Sabot, Francois, 2025, "Data used for the analysis described in GrAnnoT paper", https://doi.org/10.23708/DO1RTF, DataSuds, V6 GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the data necessary for these tests is available in this dataset. It includes mainly pangenome graphs, genomes, and annotations.
Output from the analysis described in GrAnnoT paper Oct 29, 2025 - GrAnnoT data and output Marthe, Nina; Sabot, Francois, 2025, "Output from the analysis described in GrAnnoT paper", https://doi.org/10.23708/RRSKRA, DataSuds, V6 GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the outputs from these tests are available in this dataset. It includes mainly transferred annotations.

rice data

Jul 31, 2026 - GraNPA true data

Carrette, Camille; Muller, Cédric, 2026, "rice data", https://doi.org/10.23708/M2U8UV, DataSuds, V1, UNF:6:s2YUeS/27WhTMw1SDfr03g== [fileUNF]

This dataset cointains all the output from GraNPA original paper for rice

cattle data

Jul 31, 2026 - GraNPA true data

Carrette, Camille, 2026, "cattle data", https://doi.org/10.23708/2G2DFB, DataSuds, V1

Cattle Pangenome variation graph data used in the GranPA paper

Supplementary command lines for the GraNPA paper

Jul 30, 2026 - GraNPA other codes used for the manuscript

Carrette, Camille; Muller, Cédric, 2026, "Supplementary command lines for the GraNPA paper", https://doi.org/10.23708/AU5ALD, DataSuds, V1

This file contains all the commands used for generate data and results in the GranPA paper

GranPa source code, v1

Jul 30, 2026 - GranPa Source Code

Carrette, Camille; Muller, Cédric, 2026, "GranPa source code, v1", https://doi.org/10.23708/JG96WP, DataSuds, V1

This code is the version used in the GranPa paper

SAGHAS - Sowing AGrobiodiversity to HArvest Sustainability: a multi-source database of crop species cultivated for human food

Jul 9, 2026 - DYNADIV Team

Davy, Martin; Barnaud, Adeline; Berthouly-Salazar, Cecile; Renard Delphine; Thuillet, Anne-Celine, 2026, "SAGHAS - Sowing AGrobiodiversity to HArvest Sustainability: a multi-source database of crop species cultivated for human food", https://doi.org/10.23708/LK5VUI, DataSuds, V1, UNF:6:mNCUB06Fnpj7NbK+SblAGA== [fileUNF]

Across the vast diversity of vascular plants on Earth, around 6,000 species have been used as food sources for humans. Yet, only nine crops provide more than 60% of the calories consumed worldwide. In the face of accelerating climate change, biodiversity loss, and malnutrition, t...

Supporting data and scripts produced by the GraTools software

Mar 10, 2026 - gratools

Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Supporting data and scripts produced by the GraTools software", https://doi.org/10.23708/M24LJG, DataSuds, V1

Here, we introduce GraTools (https://forge.ird.fr/diade/gratools), a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file. After a one-time graph import, GraTools enables rapid subgraph extraction, fasta sequence retrieval, and comprehensive...

Data used in the gratools paper

Mar 6, 2026 - gratools

Sabot, Francois, 2026, "Data used in the gratools paper", https://doi.org/10.23708/SOTLQU, DataSuds, V1

These are the data (mostly Pangenome variation graphs) that were used in the gratools paper only. The file is the Zenodo DOI link for the thre graphs.

Code source for GraTools v1.1.0

Mar 6, 2026 - gratools

Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Code source for GraTools v1.1.0", https://doi.org/10.23708/DXOP8N, DataSuds, V1

This code is the original source code submitted for GraTools in March 2026. This is a dump of the IRD Forge git, master branch

Data used for the analysis described in GrAnnoT paper

Oct 29, 2025 - GrAnnoT data and output

Marthe, Nina; Sabot, Francois, 2025, "Data used for the analysis described in GrAnnoT paper", https://doi.org/10.23708/DO1RTF, DataSuds, V6

GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the data necessary for these tests is available in this dataset. It includes mainly pangenome graphs, genomes, and annotations.

Output from the analysis described in GrAnnoT paper

Oct 29, 2025 - GrAnnoT data and output

Marthe, Nina; Sabot, Francois, 2025, "Output from the analysis described in GrAnnoT paper", https://doi.org/10.23708/RRSKRA, DataSuds, V6

GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the outputs from these tests are available in this dataset. It includes mainly transferred annotations.

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