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501
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501 results for “Phylogenetic tree”
Data from: Detecting the dependence of diversification on multiple traits from phylogenetic trees and trait data
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Data from: Is the tree of life the best metaphor, model or heuristic for phylogenetics?
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Core genome phylogenetic tree of two Campylobacter novaezeelandiae and four unclassified thermophilic Campylobacter isolates from Canadian agricultural surface water
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The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species
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Data from: Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods
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Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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Comparative analyses of phenotypic sequences using phylogenetic trees
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Supplementary Materials - Adaptive Tree Proposals for Bayesian Phylogenetic Inference
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Phylogenetic trees of diatom genes of horizontal descent
<p>Supplemental dataset accompanying the paper: Comprehensive and functional analysis of horizontal gene transfer events in diatoms, Vancaester et al. MBE (<a href="https://doi.org/10.1093/molbev/msaa182">https://doi.org/10.1093/molbev/msaa182</a>).<br> <br> This dataset contains all maximum-likelihood phylogenetic trees produced using IQTree (version 1.6.5) of diatom gene families which were deemed to contain horizontal gene transfer. Additionally, a file containing the gene family, donor, acceptor, the genes of the nine diatoms and the support for all events is given.</p> <p>The dataset containing the generated gene expression matrices and the defined co-expression clusters for <em>Phaeodactylum tricornutum</em> can be found on <a href="https://zenodo.org/record/3964792#.XyCCM-dCdPY">(https://zenodo.org/record/3964792#.XyCCM-dCdPY)</a></p> <p> </p>
Phylogenetic Bayesian and Maximum Likelihood trees of Mimosa clade Petiolovariabilis
<p>Bayesian tree generated on BEAST2 and Maximum likelihood on IQ-TREE, generated in the study about <em>Mimosa</em> clade <em>Petiolovariabilis</em>, based on six regions (trnD-trnT, trnL intron, trnL-trnF, trnH-psbA, ITS, and ETS).</p>
Many-core algorithms for high-dimensional gradients on phylogenetic trees
<p>XMLs, trees, and log files for "Many-core algorithms for high-dimensional gradients on phylogenetic trees". </p>
Figure 1. Maximum parsimony rooted phylogenetic tree for a in A Coronavirus Detected in the Vampire Bat Desmodus rotundus
Figure 1. Maximum parsimony rooted phylogenetic tree for a segment of the ORF1b of the Coronavirus genus, showing each of the three groups in the genus and in bold and underlined the strain BatCoV DR/2007 detected in the enteric content of a Desmodus rotundus bat. Numbers at each node are 1,000 replicates bootstrap values.
FIG 2 in Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat
FIG 2 Genome organization of NeoCoV and sequence identity compared to other clade c betacoronaviruses. (A) Genome organization of NeoCoV. The NeoCoV genome is represented by a black line; ORFs are indicated by gray arrows. The ribosomal frameshift site (RFS) is marked with an arrowhead. The locations of transcription regulatory core sequences (TRSs) following the leader (L) are marked by labeled dots and numbered in their order of appear- ance from the genomic 5= terminus. (B) Genomic sequence identity between NeoCoV and other clade c betacoronaviruses. Plots were generated by using SSE version 1.1 (25). The graph representing the comparison of the phyloge- netically basal camel virus NRCE-HKU205 and NeoCoV is not shown due to a total overlap in the curve resulting from the comparison between NeoCoV and human MERS-CoV.
FIG 1 in Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat
FIG 1 Neoromicia capensis bat. The absence of a tiny upper premolar separates it from similarly sized Pipistrellus and Hypsugo bats. The presence of an occipital helmet separates it from Neoromicia zuluensis, the species to which it was assigned based on preliminary morphological criteria.
Phylogenetic trees
<p>Phylogenetic trees from different matrix versions and under different treatments.</p>
FIGURE 7. The phylogenetic tree topology for Urocaridella arabianensis n in Urocaridella arabianensis n. sp., a new Palaemonid shrimp (Crustacea, Decapoda Palaemonidae) from Lakshadweep Islands, India with taxonomic comparison on the genus Urocaridella Borradaile, 1915
FIGURE 7. The phylogenetic tree topology for Urocaridella arabianensis n. sp. with congener species based on COI (A), 16S (B) genes sequences using Bayesian inference (BI)/maximum likelihood (ML) analyses.
FIGURE 8. The phylogenetic tree topology for Urocaridella arabianensis n in Urocaridella arabianensis n. sp., a new Palaemonid shrimp (Crustacea, Decapoda Palaemonidae) from Lakshadweep Islands, India with taxonomic comparison on the genus Urocaridella Borradaile, 1915
FIGURE 8. The phylogenetic tree topology for Urocaridella arabianensis n. sp. with congener species based on 18S (A) and H3 (B) genes sequences using Bayesian inference (BI)/maximum likelihood (ML) analyses.
FIGURE 2. Tree indicating the phylogenetic relationship inferred from 28s in Molecular approach to identify sibling species of the Ceriodaphnia cornuta complex (Cladocera: Daphniidae) from Australia with notes on the continental endemism of this group
FIGURE 2. Tree indicating the phylogenetic relationship inferred from 28s gene sequences for Ceriodaphnia cf. cornuta within Australia. Numbers above branches are Maximum likelihood (100 replicates) and numbers in bold are from Bayesian Analysis. Legends: = Species A; = Species B; = Species C.
FIGURE 1. Phylogenetic tree generated from a in Stagonosporopsis rhizophilae sp. nov. (Didymellaceae, Pleosporales), a new rhizospheric soil fungus associated with Populus deltoides Marsh
FIGURE 1. Phylogenetic tree generated from a maximum likelihood analysis based on the combined ITS, LSU, TUB, and RPB2 sequence alignment. Bayesian posterior probabilities (left, BI PP ≥ 0.50) and maximum likelihood bootstrap (right, ML BP ≥ 50) values are given at the nodes. The strains of the new fungus are highlighted in orange. Bold lines indicate BI PP = 1 and ML BP = 100. The tree is rooted with Allophoma labilis CBS 124.93, All. minor CBS 325.82, and Heterophoma adonidis CBS 114309 in gray.
Figure 6. Amphibioplana onnisi. A, RMNH.VER. 19957.a in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 6. Amphibioplana onnisi. A, RMNH.VER. 19957.a, photomicrograph of sagittal section of the anterior end, showing dorsal (de) and ventral epidermis (ve) being uniformly clothed with cilia (c); B, RMNH.VER. 19960.g, photomicrograph of horizontal section of the posterior end, showing adhesive glands (ag) discharging their secretion through the epidermis.
ScienceDex guides
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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.