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.
63
datasets available to search
ShareScore release 0.9.0
Dataset results
63 results for “Neighbor joining”
Figure. Interferon alpha-A based phylogenetic tree (neighbor joining method) constructed by MEGA 6.1 for Punjab urial in comparison with other mammalian species sequences available from GenBank (NCBI). in Characterization of interferon alpha of major histocompatibility complex class I in Punjab urial (Ovis vignei punjabiensis)
Figure. Interferon alpha-A based phylogenetic tree (neighbor joining method) constructed by MEGA 6.1 for Punjab urial in comparison with other mammalian species sequences available from GenBank (NCBI).
Fig. 1. Neighbor-joining tree generated under the Kimura 2 in Cotesia flavipes (Hymenoptera: Braconidae) as a biological control agent of sugarcane stem borers in Colombia's Cauca River Valley
Fig. 1. Neighbor-joining tree generated under the Kimura 2-parameter (K2P) nucleotide substitution model. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) is shown next to the branches. Abbreviations for sugarcane mills in Colombia's Cauca River Valley are as follows: Manuelita (MN), Mayagüez (MY), Pichichí (PC), Providencia (PV), Riopaila (RP), Risaralda (RS), Sancarlos (SC). GeneBank C. flavipes accessions:Uganda - JQ396735.1, Brazil - DQ232320.1, India - DQ232336.1, Kenya - DQ232317, Thailand - DQ232340.1, USA - DQ232330.1, South Pakistan - JQ396714.1, Jamaica - DQ232321.1, Pakistan - DQ232335.1, Sri Lanka - DQ232327.1, Indonesia - DQ232337.1, Mauritius - DQ232319.1, Reunion - DQ232329.1, Papua New Guinea - DQ232316.1.
Fig. 3. Evolutionary analysis conducted through a neighbor-joining phylogenetic tree between the cox1 in Detection of maize bushy stunt phytoplasma in leafoppers collected in native corn crops grown at high elevations in southeast Mexico
Fig. 3. Evolutionary analysis conducted through a neighbor-joining phylogenetic tree between the cox1 mini-barcode sequences obtained for the red speckled nymphs and Idiodonus wickhami (Hemiptera: Cicadellidae) (both marked with a circle) with reference sequences from GenBank. Bar 5 substitution in 100 positions.
Fig. 4. Evolutionary analysis conducted through a neighbor-joining phylogenetic tree between the 16S in Detection of maize bushy stunt phytoplasma in leafoppers collected in native corn crops grown at high elevations in southeast Mexico
Fig. 4. Evolutionary analysis conducted through a neighbor-joining phylogenetic tree between the 16S rRNA sequences amplified in this study from phytoplasma DNA, bar 1 substitution in 100 positions. Sequences in the grey square belong to the subgroup 16SrI-B. Sequences amplified from leafoppers (Hemiptera: Cicadellidae) Dalbulus elimatus marked with a circle and from Idiodonus wickhami marked with a square.
Fig. 12. A neighbor-joining tree for 10 in Fig. 45 in Fig. 23. Saiva formosana Kato, 1929, male genitalia. A in Lanternflies (Hemiptera: Fulgoridae) of Taiwan.
Fig. 12. A neighbor-joining tree for 10 species of Coenobita from the Indo-West Pacific, based on the cytochrome c oxidase subunit I (COI) gene. Probability values at the nodes represent support values. Only values> 50% are shown. For haplotype names, see table 1. Table 2. Distinguishing characters of Coenobita pseudorugosus and C. rugosus
Figure 11. Neighbor joining tree for the 16 in Description of a new Nearctic species of Tragosoma Audinet-Serville (Coleoptera: Cerambycidae: Prioninae), with species validations, new synonymies and a lectotype designation
Figure 11. Neighbor joining tree for the 16 barcodes of Tragosoma included in the dataset; each record with province or state of origin, GenBank accession number, and sample ID. Full length sequences (658 base pairs) analyzed, unless otherwise indicated in parentheses.
Fig. 4. Relationships inferred from a neighbor-joining analysis using 1179 in Revalidation and redescription of three distinct species synonymized as Plagiometriona sahlbergi (Coleoptera: Chrysomelidae: Cassidinae)
Fig. 4. Relationships inferred from a neighbor-joining analysis using 1179 base pairs of the mitochondrial Cytochrome Oxidase I gene for ten co-occurring Brazilian Cassidinae. Multiple numbers after the species name indicate clades consisting of more than one specimen.
Fig. 1. Neighbor-joining tree generated under the K2P in New combination and redescription of Brachyponera mesoponeroides Radchenko, 1993 (Hymenoptera: Formicidae: Ponerinae)
Fig. 1. Neighbor-joining tree generated under the K2P distance model, based on a dataset consisting of 438 bp sequences.
Fig. 2. Neighbor-joining tree generated under the K2P in Conspecificity of Phintella aequipeiformis Zabka, 1985 and P. lucai Zabka, 1985 (Araneae: Salticidae) confirmed by DNA barcoding
Fig. 2. Neighbor-joining tree generated under the K2P distance model, based on a dataset consisting of 851 bp sequences. Numbers beside nodes refer to bootstrap values (1000 replicates). DDBJ/Genbank accession numbers are placed before species names.
Figure 5. Neighbor-joining tree for A in Mosquito Surveillance Program Using Ovitraps Detected Aedes aegypti at the Honolulu International Airport in 2012
Figure 5. Neighbor-joining tree for A. aegypti based on COI (450bp) and ND4 (322bp) sequences. Labels are Genbank accession numbers combined with country names.
Calculating functional diversity metrics using neighbor-joining trees
<p>The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g., Rao entropy, functional dendrograms) or multidimensional spaces (e.g., convex hulls, kernel-density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e., richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers.</p> <p>We propose the use of neighbor-joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles.</p> <p>We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets.</p> <p>Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space.</p>
Calculating functional diversity metrics using neighbor-joining trees
Open the record for dataset details and reuse information.
FIGURE 1. Neighbor joining tree for 34 in Revision of the Australian Oenochroma vinaria Guenée, 1858 species-complex (Lepidoptera: Geometridae, Oenochrominae): DNA barcoding reveals cryptic diversity and assesses status of type specimen without dissection
FIGURE 1. Neighbor joining tree for 34 Australian specimens in the genus Oenochroma (Kimura 2 Parameter, built with MEGA4; all codon positions unweighted) based on sequences of the mtDNA COI gene (barcoding fragment 5'). Values above branches are bootstrap support values superior to 95%. Terminals are identified by their process ID code on BOLD.
FIGURE 1. Neighbor-joining tree derived from Cytochrome Oxidase 1 in Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx
FIGURE 1. Neighbor-joining tree derived from Cytochrome Oxidase 1 sequences showing three genetically distinct lineages of Belizean Phaeoptyx.
FIGURE 7. Neighbor-joining tree derived from Cytochrome Oxidase 1 in Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx
FIGURE 7. Neighbor-joining tree derived from Cytochrome Oxidase 1 sequences showing three genetically distinct lineages of Belizean Astrapogon.
FIGURE 1. Optimal tree inferred using the Neighbor-Joining method inferred from 550 in Paracoccus leucadendri Mazzeo & Franco in Mazzeo, Franco & Russo, 2009, a junior synonym of Paracoccus hakeae (Williams, 1985) comb. nov. (Coccomorpha: Pseudococcidae)
FIGURE 1. Optimal tree inferred using the Neighbor-Joining method inferred from 550 replicates. Shown next to the branches is the percentage of replicate trees in which the associated taxa clustered together in the bootstrap test. The tree is drawn to scale, with branch lengths in the same units as those of the genetic distances used to infer the tree. Genetic distances were computed using the p-distance method and are in the units of the number of base differences per site.
FIGURE 8. Neighbor joining Kimura 2 in A new species of Manoa Fittkau (Diptera: Chironomidae), with DNA barcodes from Xianju National Park, Oriental China
FIGURE 8. Neighbor joining Kimura 2 parameter tree based on available Pseudochironomini DNA barcodes.
FIGURE 4. Neighbor joining Kimura 2 in Two new and one newly recorded species of Polypedilum Kieffer 1912 with DNA barcodes from Oriental China (Chironomidae: Diptera)
FIGURE 4. Neighbor joining Kimura 2 parameter sub-tree generated from BOLD, scale represents K2P genetic distance.
FIGURE 22. Neighbor-joining analysis for cytochrome c oxidase I in Review of the Palearctic Atemelia Herrich-Schäffer (Lepidoptera, Yponomeutoidea, Praydidae), with description of a new leafmining species
FIGURE 22. Neighbor-joining analysis for cytochrome c oxidase I (COI) of Palaearctic Atemelia, derived from seven samples among two species based upon Kimura 2-parameter model.
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
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.