Software and Data

Available Open Data:

Following the FAIR principles, we are sharing progressively more and more data on our DATAVERSE, feel free to mine these.

Additionally, our scales collections are described in the COLISA framework which is part of the French Infrastructure for Agronomical Resources

R packages :

Tampo is an R package that facilitates analyzing micro-chemical profiles (both mono- and multi-elemental composition) from fish otoliths using a recursive partitioning approach (zoning algorithm) that can accommodate some form of user-specified constraints. It also allows extracting environmental histories from otolith based on typical elemental/isotopic sequences generated using methods such as LA-ICPMS. Micro-chemical analysis is widely used in fisheries management and fisheries biology to identify stocks and characterize fish movements but the provided functions may be considered from the more general perspective of the chronological clustering of multivariate time series using piecewise constant regressions. Tampo was developed by Matthias Vignon.

This R package estimates the effective population sizes from actual (present – sampling date) to ancestral time with a coalescent approach. VarEFF uses microsatellites data. VarEFF was developed by Natacha Nikolic.

Stand-alone software :

This program DemoDivMS is designed to predict the genetic diversity at a microsatellite DNA marker, in a finite population, for various mutation models and for variable population size. The program is very quick. It is written in Fortran and makes use of NAG numerical routines. It creates small files of the order of 50Ko.
Authors : N. Nikolic, INRAE ; C. Chevalet , INRAE

Demogenetic Modelling :

Demogenetic Individual Based Modelling of Atlantic salmon populations dynamics under exploitation and climate change. IBASAM was formerly developed by Cyril Piou, currently developed by Matthias Buoro and Amaïa Lamarins.

Demogenetic Individual Based Modelling to simulate evolution of traits and genetic architecture under sexual selection. Developed by Louise Chevalier and Jacques Labonne.

Executable Java version here: Runaway

Installation guide here.