DYNADIV Team

The main focus of DYNADIV Team is
tounderstand how biodiversity of tropical plants is shaped through evolutionary forces resulting from human and environmental impacts.

Its activity is essentially based on population genetics but also integrates a multidisciplinary approach including ecology, botany, molecular phylogenetics and anthropology. It is structured around three axes:

Evolutionary history & domestication;
Diversity & conservation;
Global changes, diversity & adaptation.

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71 to 80 of 114 Results

S1_example.fastq May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Unknown - 3.6 KB - MD5: 3bc9d9f537ea4d956c4dc7f7970e7956 Data
S1_example.txt May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Plain Text - 3.6 KB - MD5: 3bc9d9f537ea4d956c4dc7f7970e7956 Documentation
S1-IntroductionToGBS.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 3.3 MB - MD5: 09f0c52d9219dd372cf0f3c3eff8b2f5 Documentation
S1_Introduction_to_R_Passeport.html May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) HTML - 971.1 KB - MD5: 73c5daf1d31fad39ea3b274ed6a2aafc CodeDocumentation This file show a very brief introduction to R with basic command lines used to import and explore a passport data. We used the passport file associated to the GBS analysis of West-African pearl millet accessions (Berthouly-Salazar et al. 2016). This file has been created with an...
S2_filter_VCF.html May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) HTML - 1.9 MB - MD5: b8eb1f1c105a3ea55d2405931411c28e CodeDocumentation This file show an introduction to VCF filtering with GBS data using R. We used the datset of West-African pearl millet accessions (Berthouly-Salazar et al. 2016). This file has been created with an Rmarkdown file (.Rmd). The Data dictionary is included in the file.
S2-VCF-GBS.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 260.6 KB - MD5: 278cead209cb90c8c5ff6db9e3983331 Documentation This file presents an introduction to VCF filtering.
S3_GeneticDiversity.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 8.0 MB - MD5: b221ac40593882f7deb0a1a3d35b3a17 Documentation Introduction to Population Genetics for analysing the genetic diversity of crops
S3_Genetic_diversity+structure.html May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) HTML - 4.3 MB - MD5: 828d31d700d62f10b8f9fbf120f7883a CodeDocumentation In this R tutorial, we we will take a processed VCF. First, we will explore diversity through: polymorphic SNPs (required packages: adegenet), allele frequencies (required packages: adegenet), private and shared alleles (required packages: poppr), allelic richness (required packa...
S3_install.packages.R May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) R Syntax - 975 B - MD5: c7a6dda8fc71fd10aebe8212eb9edbdf Code List of packages to install for session 3 on diversity and structure analysis. To be opened with RStudio.
S3_Structure.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 3.8 MB - MD5: f5d2b43e2d5a5eefd051c29b2c68833e Documentation Introduction to Population Genetics for analysing the genetic structure of crops.

S1_example.fastq

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Unknown - 3.6 KB -

Data

S1_example.txt

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Plain Text - 3.6 KB -

Documentation

S1-IntroductionToGBS.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 3.3 MB -

Documentation

S1_Introduction_to_R_Passeport.html

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

HTML - 971.1 KB -

CodeDocumentation

This file show a very brief introduction to R with basic command lines used to import and explore a passport data. We used the passport file associated to the GBS analysis of West-African pearl millet accessions (Berthouly-Salazar et al. 2016). This file has been created with an...

S2_filter_VCF.html

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

HTML - 1.9 MB -

CodeDocumentation

This file show an introduction to VCF filtering with GBS data using R. We used the datset of West-African pearl millet accessions (Berthouly-Salazar et al. 2016). This file has been created with an Rmarkdown file (.Rmd). The Data dictionary is included in the file.

S2-VCF-GBS.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 260.6 KB -

Documentation

This file presents an introduction to VCF filtering.

S3_GeneticDiversity.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 8.0 MB -

Documentation

Introduction to Population Genetics for analysing the genetic diversity of crops

S3_Genetic_diversity+structure.html

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

HTML - 4.3 MB -

CodeDocumentation

In this R tutorial, we we will take a processed VCF. First, we will explore diversity through: polymorphic SNPs (required packages: adegenet), allele frequencies (required packages: adegenet), private and shared alleles (required packages: poppr), allelic richness (required packa...

S3_install.packages.R

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

R Syntax - 975 B -

Code

List of packages to install for session 3 on diversity and structure analysis. To be opened with RStudio.

S3_Structure.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 3.8 MB -

Documentation

Introduction to Population Genetics for analysing the genetic structure of crops.

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