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.
248
datasets available to search
ShareScore release 0.9.0
Dataset results
248 results for “tree of life”
Fig. 16 in The Amphibian Tree Of Life
Fig. 16. Tree of amphibians provided by Roelants and Bossuyt (2005). This tree reflects a maximumlikelihood analysis of 3,963 aligned positions (2,022 variable and 1,788 parsimonyinformative) of three proteincoding nuDNA genes (ca. 555 bp of RAG1, ca. 675 bp of CXCR4, ca. 1280 bp of NCX1) and ca. 1940 bp of the mitochondrial genome (part of 16S and tRNAMet, and all of tRNALeu, tRNAIle, ND1, and tRNAGln). Alignment was done initially using ClustalX (Thompson et al., 1997; presumably applying default cost functions) followed by a probabilistic method implemented in the program ProAlign (Löytynoja and Milinkovitch, 2003) and, in the case of 16S and tRNA seqments, subsequently modified manually, guided by models of secondary structure for Xenopus. Gaps were treated as missing data and ambiguously aligned sequences were excluded. The model of evolution assumed was GTR 1 G 1 I.
Fig. 18 in The Amphibian Tree Of Life
Fig. 18. Tree of Pelobatoidea and outgroups of GarcíaParís et al. (2003) based on 1,000 bp of two mitochondrial genes: cytochrome c and 16S rRNA. The sequences were aligned using Clustal X (Thompson et al., 1997) using default costs then manually modified based on published secondarystructure models of the 16S gene. Gaps were treated as missing data and data were analyzed under the assumption of the GTR 1 G substitution model, as suggested by ModelTest 3.06 (Posada and Crandall, 1998). The tree was rooted on Ascaphus montanus 1 A. truei. Quotation marks denote nonmonophyly.
Figure 5. A, topological similarities between gene trees. A in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 5. A, topological similarities between gene trees. A non-metric multidimensional ordination plot, based on the Robinson–Foulds (RF) distance between each pair of genes, is used to visualize the topological similarity among the 208 single gene trees. Pairs of gene trees with similar topologies are closer together in the two-dimensional space. Colours represent RF distances between individual gene trees and the extended majority-rule consensus (MRE) phylogeny. B, identifying optimal subsets of genes with the least topological incongruence. The graph shows the Tree Certainty (TC) values from Salichos & Rokas (2013). Information theory approach using the MRE phylogeny as a reference tree, where higher values represent greater congruency between the gene trees and the MRE tree. The x-axis represents the number of genes sampled, following an iterative procedure beginning with the first two genes in the respective ranking and progressively adding genes according to their order in the list. The five ranking criteria all outperformed random gene orders.
Figure 1 in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
Figure 1. Bioinformatic pipeline used for the identification and phylogenetic analysis of 210 single copy genes from Illumina short-read sequence data. The box with the dashed line indicates a pre-processing step that was necessary prior to assembly when sequence quality was low.
3D genomics across the tree of life reveals condensin II as a determinant of architecture type [DamID-seq]
GEO Series GSE163626. Homo sapiens. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
3D genomics across the tree of life reveals condensin II as a determinant of architecture type
GEO Series GSE163641. Homo sapiens. 29 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Evolution of the PRD1-adenovirus lineage (Varidnaviria): a viral tree of life incongruent with the cellular universal tree of life(data)
<p>Additional data for the manuscript "Evolution of the PRD1-adenovirus lineage (<em>Varidnaviria</em>): a viral tree of life incongruent with the cellular universal tree of life"</p>
AnnoTree: visualization and exploration of protein domain families across the tree of life
<p>This file is an older version of AnnoTree, published before BioArxiv first print, please do not use.</p>
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.