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103 results for “bootstrap”
text-fig. 53. Strict consensus tree resulting from the analysis of the pruned data matrix with 51 taxa. Numbers at the nodes indicate bootstrap support values in branches that have more than 50 per cent support. The consensus tree is based on 5544 trees of 652 steps (CI 0-42, RI 0-748, RCI 0-314). in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 53. Strict consensus tree resulting from the analysis of the pruned data matrix with 51 taxa. Numbers at the nodes indicate bootstrap support values in branches that have more than 50 per cent support. The consensus tree is based on 5544 trees of 652 steps (CI 0-42, RI 0-748, RCI 0-314).
FIGURE 3. Maximum Likelihood tree generated from the combined ITS and LSU sequences. Bootstrap support values above 50 in A new species of Naematelia (Tremellales, Basidiomycota) from India
FIGURE 3. Maximum Likelihood tree generated from the combined ITS and LSU sequences. Bootstrap support values above 50 are indicated above branches. The new species is indicated in bold. Holotype is represented in red color. Cryptococcus depauperatus was set as the outgroup.
Supplementary phylogenetic trees of Babesia bigemina based on partial sequences of both genes Rap-1a and gp45, with SH-aLRT support values (%), aBayes support, and ultrafast bootstrap support (%).
Open the record for dataset details and reuse information.
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support
<p>Whole genome comparisons based on Average Nucleotide Identities (ANI) and the Genome-to-genome distance calculator have risen to prominence in rapidly classifying prokaryotic taxa using whole genome sequences. Some implementations have even been proposed as a new standard in species classification and have become a common technique for papers describing newly sequenced genomes. However, attempts to apply whole genome divergence data to delineation of higher taxonomic units and to phylogenetic inference have had difficulty matching those produced by more complex phylogenetic methods. We present a novel method for generating statistically supported phylogenies of archaeal and bacterial groups using a combined ANI and alignment fraction-based metric. For the test cases to which we applied the developed approach we obtained results comparable with other methodologies up to at least the family-level. The developed method uses non-parametric bootstrapping to gauge support for inferred groups. This method offers the opportunity to make use of whole-genome comparison data, that are already being generated, to quickly produce phylogenies including support for inferred groups. Additionally, the developed ANI methodology can assist classification of higher taxonomic groups.<br> <br> Included herein are supplemental materials, and all whole genome datasets used throughout the construction of this work.</p>
FIGURE 1. The maximum likelihood majority rule consensus tree for the analyzed Pseudorobillarda and related taxa. RAxML bootstrap support values above 50 in Morphology and phylogeny of Pseudorobillarda eucalypti sp. nov., from Thailand
FIGURE 1. The maximum likelihood majority rule consensus tree for the analyzed Pseudorobillarda and related taxa. RAxML bootstrap support values above 50% (ML) are given at the nodes. Phylogeny tree is rooted to Schismatomma decolorans.
FIGURE 29. Bootstrap 50 in A new Gonatocerus (Hymenoptera: Mymaridae) from Argentina, with taxonomic notes and molecular data on the G. tuberculifemur species complex
FIGURE 29. Bootstrap 50% majority-rule consensus trees constructed with the neighbor-joining algorithm of egg parasitoid species belonging to the G. tuberculifemur complex inferred from ITS1 sequence data. Refer to the figure legend on Figs 27 and 28 for labels.
FIGURE 10. Bootstrap 50 in Phylogenetic review of dobsonflies of the subfamily Corydalinae and the genus Corydalus Latreille (Megaloptera: Corydalidae)
FIGURE 10. Bootstrap 50% majority rule consensus tree (n = 1000 replicates) from the updated phylogenetic analysis of Corydalinae genera.
FIGURE 6. Bootstrap 50 in Phylogenetic review of dobsonflies of the subfamily Corydalinae and the genus Corydalus Latreille (Megaloptera: Corydalidae)
FIGURE 6. Bootstrap 50% majority rule consensus tree (n = 1000 replicates) from the revised data matrix extracted from Glorioso (1981).
Figure 5. Agreement subtree cladogram obtained with the Ratchet algorithm for parsimonious analyses using the complete morphological matrix without gamete-related characters. Values above branches are bootstrap supports after 1000 in High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses
Figure 5. Agreement subtree cladogram obtained with the Ratchet algorithm for parsimonious analyses using the complete morphological matrix without gamete-related characters. Values above branches are bootstrap supports after 1000 replicates; values under branches are Bremer relative supports.
FIGURE 8. Bootstrap 50 in Phylogenetic review of dobsonflies of the subfamily Corydalinae and the genus Corydalus Latreille (Megaloptera: Corydalidae)
FIGURE 8. Bootstrap 50% majority rule consensus tree (n = 1000 replicates) from the revised data matrix extracted from Penny (1993).
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75 in Integrative taxonomy of Parasabella and Sabellomma (Sabellidae: Annelida) from Australia: description of new species, indication of cryptic diversity, and translocation of some species out of their natural distribution range
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75% shown on nodes. Scale bar, average of nucleotide substitutions per site.
Figure 12. Bootstrap 50 in Fragilicetus velponi: a new mysticete genus and species and its implications for the origin of Balaenopteridae (Mammalia, Cetacea, Mysticeti)
Figure 12. Bootstrap 50% majority rule strict consensus tree. Numbers above the branches are bootstrap support values. See Methods for details. Tree statistics: tree length = 1144; consistency index (CI) = 0.3086; homoplasy index (HI) = 0.6914; CI excluding uninformative characters = 0.3025; HI excluding uninformative characters = 0.6975; retention index = 0.6418; rescaled consistency index = 0.1980.
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description.
FIGURE. Bayesian tree of New Zealand spider orchids (Corybas) based on DNA sequence data from ITS, trnL-trnF and psbJ-petA. Major clades are indicated by open bars and capital letters, members of the C. trilobus aggregate are shaded, and posterior probabilities/ bootstrap percentages (≥50) indicated by numbers near each node. NI: North Island, SI: South Island, MCQI: Macquarie Island, CHI: Chatham Island in Five new species of Corybas (Diurideae, Orchidaceae) endemic to New Zealand and phylogeny of the Nematoceras clade
FIGURE. Bayesian tree of New Zealand spider orchids (Corybas) based on DNA sequence data from ITS, trnL-trnF and psbJ-petA. Major clades are indicated by open bars and capital letters, members of the C. trilobus aggregate are shaded, and posterior probabilities/ bootstrap percentages (≥50) indicated by numbers near each node. NI: North Island, SI: South Island, MCQI: Macquarie Island, CHI: Chatham Island
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site.
FIGURE. Phylogram of Panus generated from Maximum likelihood analysis of ITS sequence data. Lentinus crinitus (MK408650) was selected as the outgroup taxon. Maximum likelihood bootstrap values greater than 60% are indicated above the nodes. The new record Panus similis (HKAS 121668) is in black bold. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. Phylogram of Panus generated from Maximum likelihood analysis of ITS sequence data. Lentinus crinitus (MK408650) was selected as the outgroup taxon. Maximum likelihood bootstrap values greater than 60% are indicated above the nodes. The new record Panus similis (HKAS 121668) is in black bold.
Data for "Bootstrapping outperforms community-weighted approaches for estimating the shapes of phenotypic distributions"
<p>This repository contains datasets used in the manuscript entitled "Bootstrapping outperforms community-weighted approaches for estimating the shapes of phenotypic distributions" by Maitner et al. For details of these datasets, see https://www.authorea.com/users/244803/articles/523535-on-estimating-the-shape-and-dynamics-of-phenotypic-distributions-in-ecology-and-evolution. All datasets contain individual (and in some cases, organ-level) trait measurements.</p> <p>The dataset "all_traits_unscaled_RMBL.rds" was compiled by Christine Lamanna, Lindsey L Sloat, Andrew J. Kerkhoff, and Brian J. Enquist, Full details in https://www.authorea.com/users/244803/articles/523535-on-estimating-the-shape-and-dynamics-of-phenotypic-distributions-in-ecology-and-evolution</p> <p>The dataset "Julies_panama_data.xlsx" was compiled by Julie Messier and collaborators, full details here: https://doi.org/10.1111/j.1461-0248.2010.01476.x</p> <p>The dataset "TreefrogTadpoles.xlsx" was compiled by Nick Rasmussen, full details here: https://www.jstor.org/stable/44082203 </p> <p>The dataset "zooplankton_2019.zip" was compiled by Ewa Merz and Francesco Pomati. For more details, see www.aquascope.ch , <a href="https://github.com/mbaityje/plankifier">https://github.com/mbaityje/plankifier</a>, <a href="https://github.com/tooploox/SPCConvert">https://github.com/tooploox/SPCConvert</a>, and https://www.authorea.com/users/244803/articles/523535-on-estimating-the-shape-and-dynamics-of-phenotypic-distributions-in-ecology-and-evolution .</p>
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A in Hidden in the hills: phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species
Figure 4. ITS1 gene tree. Terminal tips have been collapsed for visualization purposes. Nodes are labelled with ultrafast bootstrap support. A full tree is available in the Supporting Information (File S1). The scale is in substitutions per site.
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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.
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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
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