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7,391 to 7,400 of 8,263 Results

JEAI GRAB(University of Abomey-Calavi and IRD) Sep 16, 2020Benin JEAI Genetic Resources & Agronomic Biodiversity in Benin (GRAB)
Benin Sep 16, 2020Partnerships
UMR EGCE(Paris-Saclay University, CNRS, IRD) Sep 11, 2020 EGCE laboratory (Evolution, Genomes, Behavior and Ecology) EGCE focuses on evolution and biodiversity. It adopts a multidisciplinary approach involving genomics, genetics and ecology at various levels, from genomes to species and even to communities. Different aspects of evolutio...
Informal waste collection system Sep 7, 2020Vietnam
Divergence_time_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 - 852 B - MD5: 3da14ba7c072d5b354c04f98edba3cc8 Code Bash script used to infer the chronogram with BEAST software. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
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...

JEAI GRAB(University of Abomey-Calavi and IRD)

Sep 16, 2020Benin

JEAI Genetic Resources & Agronomic Biodiversity in Benin (GRAB)

Benin

Sep 16, 2020Partnerships

UMR EGCE(Paris-Saclay University, CNRS, IRD)

Sep 11, 2020

EGCE laboratory (Evolution, Genomes, Behavior and Ecology) EGCE focuses on evolution and biodiversity. It adopts a multidisciplinary approach involving genomics, genetics and ecology at various levels, from genomes to species and even to communities. Different aspects of evolutio...

Informal waste collection system

Sep 7, 2020Vietnam

Divergence_time_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 - 852 B -

Code

Bash script used to infer the chronogram with BEAST software. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

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...

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