Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,663
datasets available to search
ShareScore release 0.9.0
Dataset results
3,663 results for “Phylogenetic analysis”
FIGURE 13 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 13: Dactylophysus hirtus sp. nov. A, sternite VIII; B, tergite VIII; C, sternite IX; D, tergites IX and X; E, F, aedeagus (dorsal, ventral). Abbreviation: apd, apodeme.
FIGURE 14 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 14: Dactylophysus capixabensis nom. nov. A, antenna; B, pronotum; C, D, aedeagus (ventral, dorsal).
FIGURE 28 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 28: Physodactylus patens sp. nov. A, antenna; B, head (dorsal); C, D, prothorax (dorsal, lateral); E, scutellar shield; F, G, H, pro-, meso- and metatibia; I, sternite IX; J, tergites IX and X; K, tergite VIII; L, sternite VIII; M, N, aedeagus, (dorsal, ventral).
FIGURE 34 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 34: Habitus. A, Margogastrius schneideri (13.0 mm); B, Teslasena femoralis (9.0 mm); C, T. foucarti (9.5 mm); D, Idiotropia henoni (4.5 mm); E, Oligostethius capensis (10 mm); F, Toxognathus bakeri (6.0 mm); G, T. beauchenei (9.0 mm); H, T. coomani (6.5 mm); I, T. costulatus (11.0 mm); J, T. doherty (8.0 mm); K, T. fairmairei (7.5 mm); L, T. mouhoti (5.0 mm); M, Dactylophysus hirtus sp. nov. (10.5 mm); N, D. capixabensis nom. nov. (9.0 mm); O, D. tibialis (12.0 mm); P, Heterocrepidius mendax (9.0 mm); Q, Physodactylus asper sp. nov. (9.5 mm); R, P. besckei (11.0 mm). A, D = lectotypes; E-G, I, J, L, M, P, Q = holotypes.
FIGURE 1 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 1: Margogastrius schneideri (female): A, antenna; B, C, head (anterodorsal, dorsal); D, E, F, prothorax (dorsal with head, ventral, lateral with head); G, hypomeron and pronotum; H, I, pterothorax (ventral, lateroventral); J, scutellar shield, K, L, pro- and metathoracic legs (outer surface); M, hind wing (excluding basal part); N, sternite VIII; O, tergite VIII; P, ovipositor and reproductive tract (dorsal); Q, ovipositor (ventral); R, reproductive tract (lateral). Abbreviation: a, angle of metacoxal inclination.
FIGURE 33 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 33: Dactylophysus hirtus sp. nov. A, B, C, pro-, meso- and metathoracic legs; D, apex of protibia. Physodactylus niger. E, labrum. (lateroanterior). Physodactylus henningi. F, prothoracic leg; G, protibia; H, mesothoracic leg; I, mesotibia; J, metathoracic leg; K, metatibia; L, apex of metatibia; M, lamella of protarsomere I. Physodactylus niger. N, elytral striae. Physodactylus sulcatus. O, elytral striae.
FIGURE 30 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 30: Physodactylus sulcatus. A, antenna; B, maxilla; C, labrum and mandible; D, E, prothorax (dorsal, lateral); F, G, pro and
FIGURE 25 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 25: Physodactylus latithorax sp. nov. A, antenna; B, C, D, prothorax (dorsal, ventral, lateral); E, hypomeron; F, G, pro- and metatibia; H, abdomen (ventral); I, sternite VIII; J, K, aedeagus (dorsal, ventral).
FIGURE 36 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 36: Strict consensus of four most parsimonious trees from the phylogenetic analysis of Physodactylinae (length = 281 steps, CI = 0.35, RI = 0.68). Character and state numbers are respectively above and below internodes. Black circles indicate exclusive synapomorphies and white circles homoplastic synapomorphies. Absolute Bremer support in parentheses.
FIGURE 27 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 27: Physodactylus niger. A, B, aedeagus (dorsal, ventral). Physodactylus oberthuri. C, D, aedeagus (dorsal, ventral).
FIGURE 10 in Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae)
FIGURE 10: Toxognathus costulatus. A, sternite VIII; B, tergite VIII; C, sternite IX; D, tergites IX and X; E, F, aedeagus (dorsal, ventral).
FIGURE 37. Phylogenetic results from parsimony analysis using the cranial dataset. A in A reappraisal of the cranial and mandibular osteology of the spinosaurid Irritator challengeri (Dinosauria: Theropoda)
FIGURE 37. Phylogenetic results from parsimony analysis using the cranial dataset. A, strict consensus tree of 153 MPTs retained from an equal weighting analysis (see Methods for details); B, reduced consensus tree, pruning wild card taxa from the strict consensus. Wild card taxa are highlighted with coloured boxes in A, and their possible topological positions are shown with same coloured squares in B. Important clades are labelled.
FIGURE 36. Phylogenetic results from parsimony analysis using the full dataset. A in A reappraisal of the cranial and mandibular osteology of the spinosaurid Irritator challengeri (Dinosauria: Theropoda)
FIGURE 36. Phylogenetic results from parsimony analysis using the full dataset. A, strict consensus tree of 8184 MPTs retained from an equal weighting analysis (see methods for details); B, partial reduced consensus tree, showing the clade Spinosauridae after removal of the taxon Vallibonavenatrix; C, strict consensus tree of 406 MPTs retained from an implied weighting analysis using a concavity constant of k=10 (see Methods for details). Important clades are labelled. Irritator as the main focus of our study is highlighted in bold face within the clade Spinosauridae.
Data and scripts for: Bayesian Phylogenetic Analysis on multi-core Compute Architectures: Implementation and evaluation of BEAGLE in RevBayes with MPI
<p>Phylogenies are central to many research areas in biology and commonly estimated using likelihood-based methods. Unfortunately, any likelihood-based method, including Bayesian inference, can be restrictively slow for large datasets–with many taxa and/or many sites in the sequence alignment–or complex substitution models. The primary limiting factor when using large datasets and/or complex models in probabilistic phylogenetic analyses is the likelihood calculation, which dominates the total computation time. To address this bottleneck, we incorporated the high-performance phylogenetic library BEAGLE into RevBayes, which enables multi-threading on multi-core CPUs and GPUs, as well as hardware-specific vectorized instructions for faster likelihood calculations. Our new implementation of RevBayes+BEAGLE retains the flexibility and dynamic nature that users expect from vanilla RevBayes. Additionally, we implemented a native parallelization within RevBayes without an external library using the message passing interface (MPI); RevBayes+MPI. We evaluated our new implementation of RevBayes+BEAGLE using multi-threading on CPUs and a powerful NVidia Titan V GPU against our native implementation of RevBayes+MPI. We found good improvements in speedup when multiple cores were used with up to 20-fold speedup when using multiple CPUs and over 90-fold speedup when using multiple GPU cores. The improvement depended on the data type used, DNA or amino acids, and the size of the alignment, but less on the size of the tree. We additionally investigated the cost of rescaling partial likelihoods to avoid numerical underflow and showed that unnecessarily frequent rescaling can increase runtimes 2.5 to 3-fold. Finally, we presented and compared a new approach to store partial likelihoods on branches instead of nodes which can speed up computations but comes at twice the memory requirements.</p> <p>Availability: The software described in the paper is available at https://github.com/revbayes/revbayes with documentation and tutorials found at https://revbayes.github.io.</p>
Data & Analysis Script for: Phylogenetic relatedness to native congeners drives insect abundance and diversity hosted by non-native trees
<p>The dataset contains all necessary data to reproduce the findings presented in Schweiger et al. 2023 - Phylogenetic relatedness to native congeners drives insect abundance and diversity hosted by non-native trees (submitted).</p> <p>The code necessary to reproduce the findings is included within this repository. The code contains comments. Please note, if you want to reproduce the findings you will have to change file path information matching your personal computer to be able to re-run the code.</p> <p>This data includes the biodiversity raw data collected for the manuscript. It <strong>does not </strong>include data used to calculate geographic, climatic or phylogenetic distances, as these data are freely available and necessary information to reproduce calculations are given within the Material & Methods section.</p> <p>All data is provided within one Excel file. Please, pay attention to the provided ReadMe sheet containing metadata information on the dataset.</p> <p>Please carefully read provided information within ReadMe, Metadata and Code description.</p>
Fig. 3. Phylogenetic trees from reported 18S in Molecular systematics analysis of Lymantria dispar based on 18S rRNA and cox1 mtDNA sequence data
Fig. 3. Phylogenetic trees from reported 18S rRNA genes of insects according to NJ. A. Based on sequences of full-length. B. Based on second conserved region.
Fig. 6 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 6. Termination-associated sequences (TAS), conserved sequence blocks (CSB-1, CSB-2, and CSB-3) and central conserved sequences (CSB-D) and GTGGG box in control region of two Oxyurichthys species mitogenomes.
Fig. 8 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 8. Phylogenetic trees of goby derived from Maximum Likelihood (ML) method based on 13 PCGs + 2 rRNAs. The numbers at nodes are ultrafast bootstrap values. GenBank accession numbers are placed in front of species names.
Fig. 7 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 7. Phylogenetic trees of goby derived from Bayesian Inference (BI) method based on 13 PCGs + 2 rRNAs. The numbers at nodes are posterior probability values. GenBank accession numbers are placed in front of species names.
Fig. 5 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 5. The putative origin of L-strand replication (OL) of Oxyurichthys ophthalmonema (a) and Oxyurichthys microlepis (b).
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.