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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61 to 70 of 102 Results

GBS-chr2_raw.vcf.gz May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Gzip Archive - 53.7 MB - MD5: 7ac07ce9f286e974d6c5c572c40f78d8 Data VCF file containing the raw genomic data of pearl millet. This data file is associated with the script "S2_filter_VCF.html".These data are published in Berthouly-Salazar et al. (2016).
Introduction.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 1.8 MB - MD5: fdde654296e7c56ad70fd3ee0a2ea070 Documentation This file presents the course, its objectives and the context in which it was implemented.
millet_filtered.vcf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) text/vcard - 34.5 MB - MD5: 6eab73245746d73169f90b8141511fa0 Data VCF file containing the genomic data of the pearl millet. This data file is associated with the script "S3_Genetic_diversity+structure.html".These data are published in Berthouly-Salazar et al. (2016).
millet_metadata.tab May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Tabular Data - 2.5 KB - 5 Variables, 55 Observations - UNF:6:LNg1C4IBq05VUN9bbZDOeQ== Data Table containing the passport data of the pearl millet accessions in the VCF file. This data file is associated with the script "S3_Genetic_diversity+structure.html". These data are published in Berthouly-Salazar et al. (2016).
S1_Download_R.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 288.7 KB - MD5: dbbdb9df803c84725df9ff5b4abc42f7 Documentation This file is a tutorial for installing R and RStudio.
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.

GBS-chr2_raw.vcf.gz

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

Gzip Archive - 53.7 MB -

Data

VCF file containing the raw genomic data of pearl millet. This data file is associated with the script "S2_filter_VCF.html".These data are published in Berthouly-Salazar et al. (2016).

Introduction.pdf

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

Adobe PDF - 1.8 MB -

Documentation

This file presents the course, its objectives and the context in which it was implemented.

millet_filtered.vcf

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

text/vcard - 34.5 MB -

Data

VCF file containing the genomic data of the pearl millet. This data file is associated with the script "S3_Genetic_diversity+structure.html".These data are published in Berthouly-Salazar et al. (2016).

millet_metadata.tab

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

Tabular Data - 2.5 KB - 5 Variables, 55 Observations -

Data

Table containing the passport data of the pearl millet accessions in the VCF file. This data file is associated with the script "S3_Genetic_diversity+structure.html". These data are published in Berthouly-Salazar et al. (2016).

S1_Download_R.pdf

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

Adobe PDF - 288.7 KB -

Documentation

This file is a tutorial for installing R and RStudio.

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.

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