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242 results for “maximum likelihood”
FIGURE 1. Maximum likelihood phylogenetic tree generated from combined 5.8S in A new addition to the Helvella macropus group (Helvellaceae) from Southwestern China
FIGURE 1. Maximum likelihood phylogenetic tree generated from combined 5.8S+ITS2, LSU, tef-1α, and hsp90 sequenced dataset. Maximum likelihood bootstrap (ML-BP) ≥ 70% and Bayesian posterior probabilities (BI-PP) ≥ 0.95 are indicated above the nodes. Specimen vouchers are noted after the species names. New samples collected in this study are indicated in red. Type specimens are in bold.
Figure 2. A, maximum likelihood tree inferred from 18S in Morphological, ontogenetic, and molecular investigations of freshwater hypotrich ciliates from China revealed a new genus Heterodeviata gen. nov. (Protista: Ciliophora), and a novel limnetic population of Deviata multilineae
Figure 2. A, maximum likelihood tree inferred from 18S rRNA gene sequences, showing the phylogenetic positions of the two newly sequenced species. Numbers near the nodes represent the ML bootstrap support and BI posterior probability values. Fully supported (100%/1.00) branches are marked with solid circles. 'Asterisks' indicate disagreement between the ML and BI trees. Sequences newly obtained are in pink. The scale bar corresponds to one substitution per 100 nucleotide positions. B, the tree is made referring to the ML tree in a radiation view, showing the likely systematic relationship of Heterodeviata with related genera. C, topology of species within Deviatidae in Bayesian inference (BI) tree. '**' indicates the sequence Perisincirra sp. (KY855575) is probably misidentified, which should be conspecific with Deviata brasiliensis.
FIGURE4. Maximum-likelihood tree inferred from 694 bp of COI using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes. in --Molecular--and--acoustic--evidence--support--the--species--status--of--Anthus rubescens rubescens and--Anthus [rubescens] japonicus--(Passeriformes:--Motacillidae)
FIGURE4. Maximum-likelihood tree inferred from 694 bp of COI using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes.
FIGURE3. Maximum-likelihood tree inferred from 998 bp of CR using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes. in --Molecular--and--acoustic--evidence--support--the--species--status--of--Anthus rubescens rubescens and--Anthus [rubescens] japonicus--(Passeriformes:--Motacillidae)
FIGURE3. Maximum-likelihood tree inferred from 998 bp of CR using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes.
FIGURE 1. Maximum likelihood tree from combined ITS and tub2 in Additions to Peroneutypa (Diatrypaceae, Xylariales): Introducing P. nayariophyti sp. nov. and new host associations of P. scoparia from northern Thailand
FIGURE 1. Maximum likelihood tree from combined ITS and tub2 sequence data. Bootstrap support values ≥ 60% and Bayesian posterior probabilities ≥ 0.90 are indicated at the branches. The tree is rooted with Xylaria polysporicola (FCATAS848) and X. hypoxylon (CBS 122620). The taxa originating from this study are shown in blue. Type species are in bold.
Data from: Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes
Open the record for dataset details and reuse information.
Data from: Generic recircumscriptions of Oncidiinae (Orchidaceae: Cymbidieae) based on maximum likelihood analysis of combined DNA datasets
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Data from: A maximum likelihood approach to generate hypotheses on the evolution and historical biogeography in the Lower Volga Valley regions (southwest Russia)
Open the record for dataset details and reuse information.
Figure 4. Optimal maximum-likelihood tree resulting from the RAxML analysis. Bootstrap support values greater than 50 in Taxonomy of Micronesian monitors (Reptilia: Squamata: Varanus): endemic status of new species argues for caution in pursuing eradication plans
Figure 4. Optimal maximum-likelihood tree resulting from the RAxML analysis. Bootstrap support values greater than 50% are shown on the nodes. Scale bar corresponds to the mean number of nucleotide substitutions per site.
MCMC Chains and Maximum Likelihood Parameters for a Random Walk Model of Dark Matter Halo Spins
<p>MCMC chains and the maximum likelihood model parameter file associated with the random walk dark matter halo spin model of Benson, Behrens, & Lu (2020; https://arxiv.org/abs/2001.09208). See the README file for details.</p>
Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf
<p>Ludt et al. 2020, Fig. S1: Phenetic tree of sequence similarity constructed using a maximum likelihood approach for mtDNA COI sequences from the EAD survey of the bony-fish species of the Arabian Gulf.</p> <p>Ludt, W.B., Jabado, R.W., Al Hameli, S.M., Freeman, L., Teruyama, G., Chakrabarty, P. & Al Dhaheri, S.S. (2020) Establishing a reference collection and DNA barcoding the coastal fishes of the United Arab Emirates. <em>Journal of the Ocean Science Foundation</em>, 35, 54–64.</p>
Fig. 55. Maximum likelihood tree inferred from ITS2 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Fig. 55. Maximum likelihood tree inferred from ITS2 gene of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3–4 = ABGD with initial partitions (IP); 5–7 = ABGD with recursive partitions (RP); 8 = GMYC yule analysis; 9 = GMYC coalescent analysis; 10 = bPTP with ML; 11 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers on branches correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.
MCMC Chains and Maximum Likelihood Parameters for a Random Walk Model of Dark Matter Halo Concentrations
<p>MCMC chains and the maximum likelihood model parameter file associated with the random walk dark matter halo concentration model of Johnson, Benson, & Grin (2020; https://arxiv.org/abs/2006.15231). See the README file for details.</p>
Data from: Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics
Since their advent, supertrees have been increasingly used in large-scale evolutionary studies requiring a phylogenetic framework and substantial efforts have been devoted to developing a wide variety of supertree methods (SMs). Recent advances in supertree theory have allowed the implementation of maximum likelihood (ML) and Bayesian SMs, based on using an exponential distribution to model incongruence between input trees and the supertree. Such approaches are expected to have advantages over commonly used non-parametric SMs, e.g. matrix representation with parsimony (MRP). We investigated new implementations of ML and Bayesian SMs and compared these with some currently available alternative approaches. Comparisons include hypothetical examples previously used to investigate biases of SMs with respect to input tree shape and size, and empirical studies based either on trees harvested from the literature or on trees inferred from phylogenomic scale data. Our results provide no evidence of size or shape biases and demonstrate that the Bayesian method is a viable alternative to MRP and other non-parametric methods. Computation of input tree likelihoods allows the adoption of standard tests of tree topologies (e.g. the approximately unbiased test). The Bayesian approach is particularly useful in providing support values for supertree clades in the form of posterior probabilities.
Fig. 3. Maximum likelihood gene trees estimated using PhyML. A in Morphological and Genetic Characterization of the First Species of Thalassodrilides (Annelida: Clitellata: Naididae: Limnodriloidinae) from Japan
Fig. 3. Maximum likelihood gene trees estimated using PhyML. A, COI; B, ITS. Numbers at branches denote aLRT branch support. Scale shows estimated numbers of nucleotide substitutions per site.
Fig. 3. Maximum likelihood phylogeny for 72 unique haplotypes obtained from O. hatcheri, O in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals
Fig. 3. Maximum likelihood phylogeny for 72 unique haplotypes obtained from O. hatcheri, O. bonariensis, and O. smitti. Haplotype labels indicate their sampling locality (as explained in Fig. 1 and Table 1) and the number of individuals (in parentheses). Several common haplotypes were recovered from several individuals from the same or different localities (most significantly haplotype 5). Monophyly of haplotypes from each species is supported by 100% bootstrap values, and two groups of O. hatcheri haplotypes (from EPU and CDP, indicated by heavier lines) also received strong bootstrap support. All other nodes were weakly supported by bootstrap analyses. *: presumptive hybrids individuals identified on meristic and morphological characters (Table 2).
Fig. 2. Maximum Likelihood tree for genus Fusicolla with RPB2 dataset. Node numbers indicate bootstrap value above 70 in First report of seven unrecorded bambusicolous fungi in Korea
Fig. 2. Maximum Likelihood tree for genus Fusicolla with RPB2 dataset. Node numbers indicate bootstrap value above 70%. Blue colored name indicates the strains isolated in this study. Type strains are indicated by "T".
Fig. 2. Maximum likelihood 16S in Molecular Identification of a Phage-infected Protochlamydia Strain Naturally Harboured by Non-Encysting Naegleria
Fig. 2. Maximum likelihood 16S rDNA tree of Parachlamydiaceae, showing the major lineages and sublineages, and all the phylotypes assigned to Protochlamydia naegleriophila. The Pcb1 strain recovered here and the reference strain KNic (in bold) are both natural endosymbionts of Naegleria spp. The tree was rooted on members of Criblamydiaceae and Waddliaceae. Bootstrap values (BV) after 1,000 replicates for ML/NJ/MP were indicated at nodes. Filled circle – node 100% supported with all three methods; asterisk – node supported but BV <40%; hyphen – node not supported. Scale bar represents substitution/site.
Fig. 4. Bootstrap consensus tree inferred from 1000 replicates, using the Maximum Likelihood method. The analysis involved 20 in Severe coenurosis caused by larvae of Taenia serialis in an olive baboon (Papio anubis) in Benin
Fig. 4. Bootstrap consensus tree inferred from 1000 replicates, using the Maximum Likelihood method. The analysis involved 20 sequences of 12S rDNA gene of cestodes having coenurus type larvae (Taenia serialis and T. multiceps) and one sequence of Echinococcus granulosus, as outgroup. For each sequence, the GenBank Accession number, species, developmental stage, host and geographic origin are provided. A total of 320 positions were included in the dataset. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches.
Fig. 5 Maximum Likelihood inferred relationships for all the trnD1–4 in An exceptional case of mitochondrial tRNA duplication-deletion events in blood-feeding leeches
Fig. 5 Maximum Likelihood inferred relationships for all the trnD1–4 sequences known to date
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.