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50 results for “MOTUs”
mOTUs 1.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
<strong>Software: </strong>mOTUs<br><strong>SoftwareVersion: </strong>1.1<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> http://www.bork.embl.de/software/mOTUs1/<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:motu<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> mOTU.v1.padded<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:motu
mOTUs 2.5.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
<strong>Software: </strong>mOTUs<br><strong>SoftwareVersion: </strong>2.5.1<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://motu-tool.org/<br><strong>DockerImage:</strong> cami/motus:2.5.1<br><strong>IsBiobox:</strong> False<br><strong>ReferenceDatabase:</strong> mOTUs database version 2.5.0<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> for i in {0..63}; do motus profile -f sample_$((i))/reads/anonymous_reads_r1.fq -r sample_$((i))/reads/anonymous_reads_r2.fq -n $((i)) -C precision > sample$((i)).profile ; done<br>cat sample*.profile > cami2_mouse_gut_motus2.5.1.profile
NCBI taxonomy dump used for specI and mOTUs
<p>NCBI taxonomy dump used for:</p> <p>- mOTUs 2.5.0</p> <p>- progenomes 2</p>
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions
FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]
BOLD Insecta and Araneae data files for "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs"
<p>These are the BOLD Insecta and Araneae DWC files for use with the automated scripting procedure from "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs".</p>
Supplementary material 9 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Unique continent and island hit combinations in Insecta dataset
Supplementary material 8 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Number of distinct continent or island groupings recovered per Insecta BIN
Supplementary material 7 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
List of intercontinental and island Insecta BINs with identification metadata
Supplementary material 6 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Intercontinental and island records for targeted Platygastroidea in GBIF and the literature
Supplementary material 4 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Platygastroidea COI dataset NJ tree.tre
Supplementary material 2 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Randomized BOLD BINs for validation of the Insecta dataset
Supplementary material 19 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Randomized BOLD BINs for validation of the Araneae dataset
Supplementary material 18 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
List of intercontinental and island Araneae BINs with identification metadata
Supplementary material 3 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Intercontinental and island Platygastroidea COI dataset alignment
Supplementary material 17 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Platygastroidea BIN identifications using digital morphology infrastructure
Supplementary material 16 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Pairwise geographic hit comparisons for the Trissolcus BIN, GBIF, and literature dataset
Supplementary material 14 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Pairwise geographic hit comparisons for the Synopeas BIN, GBIF, and literature dataset
Supplementary material 13 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Pairwise geographic hit comparisons for the Platygaster BIN, GBIF, and literature dataset
Supplementary material 12 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Pairwise geographic hit comparisons for the Platygastroidea BIN, GBIF, and literature dataset
Supplementary material 15 from: Moore MR, Talamas EJ, Bremer JS, McGathey N, Fulton JC, Lahey Z, Awad J, Roberts CG, Combee LA (2023) Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs. NeoBiota 88: 169-210. https://doi.org/10.3897/neobiota.88.106326
Pairwise geographic hit comparisons for the Telenomus BIN, GBIF, and literature dataset
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.