UMR MIVEGEC

Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control

The aims of the group MIVEGEC are to develop integrative and transdisciplinary research to the mechanisms that maintain, amplify and transmit pathogenic agents, along with their genetic and epigenetic determinants, in order to better understand how these systems evolve and to improve their control.

L’UMR MIVEGEC "Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle" a pour mission de comprendre, via des recherches intégratives et transdisciplinaires, les mécanismes de maintenance, d’amplification et de transmission d’agents pathogènes, leurs déterminants génétiques et non génétiques, afin de pouvoir mieux appréhender l’évolution de ces systèmes infectieux et contribuer à en améliorer le contrôle.

Porpoises genetics and genomics

REACT Project

REACT2 Project

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211 to 220 of 223 Results

Divergence_time_beast.xml Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum XML - 1.1 MB - MD5: 123ff8c0bc59283a8a6364798a24e81c Data Input file used in the script Divergence_time_beast.sh which uses BEAST software to infer the chronogram (divergence time estimates). This file was created with BEAUti program of BEAST. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
jmodeltest.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 826 B - MD5: 083b0144bee47b1ffbc55d8aa77b23e6 Code Bash script used to run JmodelTest2 to infer the best substitution model. The results generated by JmodelTest2 were subsequently used in the phylogenetic reconstruction, the skyline plot and the inference of the chronogram. More information is provided in Ben Chehida et al. (2020...
Mitobim.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 1.4 KB - MD5: db521dc52342ba5bb7328c4d44aaf39b Code Bash script used to assemble mitogenomes from MiSeq 100PE reads using MITOBIM. It generates a fasta file for each individual assembled. More information is provided in Text S2 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
Pi_rarefaction.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 2.2 KB - MD5: f2c8d5171b65ec11dfa709337923b1b1 Code Shell wrapper that calculates the nucleotide diversity using a rarefaction method and the infoseq_diversity function from libDiversity (provided in this data archive as a courtesy of the author, Guillaume Achaz (guillaume.achaz[at]mnhn.fr). See details in Ben Chehida et al. (2020...
porpoise_mitogenome_final_alignment.fasta Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Unknown - 1.0 MB - MD5: e8d15f7d21d09a589396bbd2fe8d4e9a Data Final multiple sequences alignment (fasta format) of 16,302 base pairs (bps) for 71 cetacean mitogenomes. It includes 63 porpoises and 7 outgroup sequences. The porpoise mitogenomes were assembled from short read MiSeq 100PE with MITOBIM and Geneious. The assembled fasta sequence...
random_number.py Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Python Source Code - 1.2 KB - MD5: acfd75a55d7296be44e476b842408231 Code Python script used to select randomly sequences from a fasta file. This script is used to conduct the rarefaction analysis. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9).
skyline_beast.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 872 B - MD5: 55a14528fb89152ed013e14964f94266 Code Bash script used to run BEAST software and reconstruct the skyline plots. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
skyline_file.xml Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum XML - 198.1 KB - MD5: 820c82a0bb4b3688607eaa051a8a6375 Data Input file used in skyline_beast.sh to run the skyline plot analysis in BEAST software which estimates the variation of the effective population size through time. This file was created with BEAUti program of BEAST See details in Ben Chehida et al. (2020, Scientific Reports, DOI:...
Trimmomatics.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 1.3 KB - MD5: a2cc3c42e514b85eb265f66c33f2a88c Code Bash script used to clean the raw read (fastq format) with trimmomatic. Additional information is provided in Text S1 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
Porpoises genetics and genomics Aug 31, 2020 The Porpoises genetics and genomics dataverse gathers together data and scripts from the porpoise ecological and evolutionary genetics & genomics project. This project aims at advancing our knowledge regarding the ecology and evolution of the seven species of porpoises (Phocoenid...

Divergence_time_beast.xml

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

XML - 1.1 MB -

Data

Input file used in the script Divergence_time_beast.sh which uses BEAST software to infer the chronogram (divergence time estimates). This file was created with BEAUti program of BEAST. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

jmodeltest.sh

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Shell Script - 826 B -

Code

Bash script used to run JmodelTest2 to infer the best substitution model. The results generated by JmodelTest2 were subsequently used in the phylogenetic reconstruction, the skyline plot and the inference of the chronogram. More information is provided in Ben Chehida et al. (2020...

Mitobim.sh

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Shell Script - 1.4 KB -

Code

Bash script used to assemble mitogenomes from MiSeq 100PE reads using MITOBIM. It generates a fasta file for each individual assembled. More information is provided in Text S2 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

Pi_rarefaction.sh

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Shell Script - 2.2 KB -

Code

Shell wrapper that calculates the nucleotide diversity using a rarefaction method and the infoseq_diversity function from libDiversity (provided in this data archive as a courtesy of the author, Guillaume Achaz (guillaume.achaz[at]mnhn.fr). See details in Ben Chehida et al. (2020...

porpoise_mitogenome_final_alignment.fasta

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Unknown - 1.0 MB -

Data

Final multiple sequences alignment (fasta format) of 16,302 base pairs (bps) for 71 cetacean mitogenomes. It includes 63 porpoises and 7 outgroup sequences. The porpoise mitogenomes were assembled from short read MiSeq 100PE with MITOBIM and Geneious. The assembled fasta sequence...

random_number.py

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Python Source Code - 1.2 KB -

Code

Python script used to select randomly sequences from a fasta file. This script is used to conduct the rarefaction analysis. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9).

skyline_beast.sh

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Shell Script - 872 B -

Code

Bash script used to run BEAST software and reconstruct the skyline plots. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

skyline_file.xml

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

XML - 198.1 KB -

Data

Input file used in skyline_beast.sh to run the skyline plot analysis in BEAST software which estimates the variation of the effective population size through time. This file was created with BEAUti program of BEAST See details in Ben Chehida et al. (2020, Scientific Reports, DOI:...

Trimmomatics.sh

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Shell Script - 1.3 KB -

Code

Bash script used to clean the raw read (fastq format) with trimmomatic. Additional information is provided in Text S1 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

Porpoises genetics and genomics

Aug 31, 2020

The Porpoises genetics and genomics dataverse gathers together data and scripts from the porpoise ecological and evolutionary genetics & genomics project. This project aims at advancing our knowledge regarding the ecology and evolution of the seven species of porpoises (Phocoenid...

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