In silico: databases and models

METAPOP

Simulation platform.
Metapop simulates the evolution of meta-populations of monoecious plants across heterogeneous landscapes. Based on the theory of quantitative genetics, Metapop describes individuals with an explicit representation of their genetics and spatial position. Its structure comprises several interacting modules. Metapop, developed at UMR BIOGECO, is a free software under the GNU General Public License version 3.

https://quercusportal.pierroton.inra.fr/metapop/metapop-user-documentation.pdf

Antoine Kremer

PINUS PORTAL

Web portal for access to genomic and genetic resources on Pinaceae. The portal provides access to 5 separate databases (PINUSMAP, GD², CMap, EST, TREEPOP). A static section of the portal is dedicated to general information on the genus Pinus.

https://pinusportal.pierroton.inra.fr

François Ehrenmann

QUERCUS PORTAL

Web portal for access to genomic and genetic resources on fagaceae. The portal provides access to 9 different databases (QUERCUSMAP, GD², CMap, EST, TREEPOP, OAK PROVENANCE, SSR, CANDIDATE GENES, SNP). A static section of the portal is dedicated to general information on the genus Quercus.

https://quercusportal.pierroton.inra.fr

François Ehrenmann

PINELINE

Web application / database for the storage of daily micro-variation data of maritime pine and associated environmental data (internal Biogeco access only).

http://pineline.pierroton.inra.fr/pineline/

François Ehrenmann

PGD BIOGECO

• Web interface for entering data sets and metadata, as part of the unit's PGD (intranet access)
• Unit DMP and data flow diagram of the UMR (intranet access)

• http://147.100.113.193/pgd-biogeco/
• http://147.100.113.193/pgd-biogeco/docs/logigramme_origine.html

François Ehrenmann / Philippe Chaumeil

R-SYST

Shared database between EFPA & SPE of barcoding/metabarcoding reference databases for a variety of organisms of interest to INRA.

http://www.rsyst.inra.fr

Alain Franc

OAK GENOME

Web application: website concerning the sequencing of the oak genome and identification of genes important for the adaptation of forest trees.

http://www.oakgenome.fr/

François Ehrenmann

CAVISOFT

Data acquisition, control and analysis software dedicated to cavitron instruments.

http://sylvain-delzon.com/caviplace/cavisoft/

Régis Burlett

DISSEQ, DEKAM

C programs for calculating distances between sequences using the Smith-Waterman algorithm; parallelized version in MPI

Alain Franc

METABARCODING SUITE

Set of python programs for supervised and unsupervised learning in metabarcoding (environmental samples); declic for baseline analysis (molecular/morphological dictionary); diagno-syst for supervised learning; yapotu for building OTUs (unsupervised learning)

Alain Franc

FaMoz

Software for parentage analysis based on dominant and codominant genetic markers. Published in 2003, still has a tiny life.

http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/

Sophie Gerber