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242 results for “Maximum Likelihood”
FIGURE 1. Maximum likelihood phylogenetic tree generated from a in Type studies on two Paxillus species (Paxillaceae, Boletales) described from China
FIGURE 1. Maximum likelihood phylogenetic tree generated from a three-locus (nrLSU, ITS, and tef1-α) dataset of the Boletinellus species. ML bootstrap (BS>50 %) are indicated above the branches. Voucher specimens and localities where the specimens were collected are provided. The new combination is in bold.
◂Fig. 2 Maximum likelihood trees. A Tree obtained when analysing 18S data set. B Tree obtained when analysing 28S data set. C Tree obtained when analysing COI data set. D Tree obtained when analysing 16S data set. Bootstrap support values below nodes. Syllis and Typosyllis species as they were originally described in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan
◂Fig. 2 Maximum likelihood trees. A Tree obtained when analysing 18S data set. B Tree obtained when analysing 28S data set. C Tree obtained when analysing COI data set. D Tree obtained when analysing 16S data set. Bootstrap support values below nodes. Syllis and Typosyllis species as they were originally described
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown. in A revised phylogenetic classification of tribe Phyllantheae (Phyllanthaceae)
FIGURE. (A) Summary phylogeny showing relations between genera in tribe Phyllantheae from Bayesian and Maximum Likelihood analysis of five markers (ITS, PHYC, accD–psaI, trnS–trnG, matK), modified from Appendix 1. Classification is shown of genera (right column), subgenera (middle column) and sections (except for the genus Phyllanthus. Sections not included in phylogenetic analyses and those for the genus Flueggea were omitted. (B) summary phylogeny of the genus Phyllanthus as envisioned here with subgenera and sections of groups included in phylogenetic studies shown.
FIGURE 1. Maximum likelihood phylogenetic tree inferred from a in Additions to Fitzroyomyces (Stictidaceae, Ascomycota) from Yunnan Province, China
FIGURE 1. Maximum likelihood phylogenetic tree inferred from a combined dataset of LSU, ITS and mtSSU. The tree has been artificially rooted with Orceolina kerguelensis, Placopsis perrugosa and Trapelia placodioides sequences. Newly isolated strains are indicated in red bold font. Bootstrap support values for maximum likelihood (ML) equal to or higher than 60% and Bayesian Probability (BYPP) equal to or higher than 0.90 are mentioned above/below the branches.
Training data for 'Maximum Likelihood Phylogeny Reconstruction'' (Galaxy Training Material)
<p>This data is used for Galaxy Training Network (GTN) training 'Maximum Likelihood Phylogeny Reconstruction'. It consists of 173 amino acid alignments of orthologs found in chromosome 5 of four strains of S. cerevisiae. Original sequence data (https://zenodo.org/record/6610704) was processed in Galaxy following GTN 'Preparing genomic data for phylogeny reconstruction' training (10.48546/workflowhub.workflow.359.1) to generate alignments of orthologs.</p>
FIGURE 2. Maximum likelihood tree estimated from the COI1 in Molecular identification of Isospora coerebae Berto, Flausino, Luz, Ferreira & Lopes, 2010 (Chromista: Miozoa: Eimeriidae) from the bananaquit Coereba flaveola (Linnaeus, 1758) (Passeriformes: Thraupidae: Coerebinae) from Brazil
FIGURE 2. Maximum likelihood tree estimated from the COI1 gene sequences of coccidian species. Numbers at the nodes show posterior probabilities under the Bayesian Inference analysis/bootstrap values derived from Maximum Likelihood analysis. Scale bar represents the number of nucleotide substitutions per site.
FIGURE 3. Maximum likelihood tree estimated from the COI2 in Molecular identification of Isospora coerebae Berto, Flausino, Luz, Ferreira & Lopes, 2010 (Chromista: Miozoa: Eimeriidae) from the bananaquit Coereba flaveola (Linnaeus, 1758) (Passeriformes: Thraupidae: Coerebinae) from Brazil
FIGURE 3. Maximum likelihood tree estimated from the COI2 gene sequences of coccidian species. Numbers at the nodes show posterior probabilities under the Bayesian Inference analysis/bootstrap values derived from Maximum Likelihood analysis. Scale bar represents the number of nucleotide substitutions per site.
FIGURE 1. Maximum likelihood phylogram inferred from 53 taxa from ITS and 28S in Expanding the diversity of mucoralean fungi from northern Thailand: novel Backusella species from soil
FIGURE 1. Maximum likelihood phylogram inferred from 53 taxa from ITS and 28S genetic markers. Bootstrap support (BS) from RAxML and IQ-tree, and the posterior probability from Bayesian analysis are provided near the nodes as BS/BS (IQ-tree)/ PP. Values <70% for bootstrap support and <0.80 for posterior probability are indicated by a minus sign (–). Unrecovered branching is indicated by (*) sign. The novel strain proposed in the current study is shown in bold. T, ET, LT, and NT indicate ex-type, ex-epitype, ex-lectotype and ex-neotype strains, respectively. Mucor indicus (CBS 226.29) and M. koreanus (EML-QT1) were used as outgroup taxa.
FIGURE 7. Maximum likelihood trees. A in Descriptions of two new species of Armatoplana (Polycladida: Stylochoplanidae) from the coasts of Japan, with their phylogenetic positions in Leptoplanoidea
FIGURE 7. Maximum likelihood trees. A, ML tree based on Dataset 2 (32 terminal taxa, 2768 bp, 17% missing data); B, ML tree based on Dataset 3 (28 terminal taxa, 2776 bp, 9% missing data). The Armatoplana species in the tree are presented in bold. For clades that received either ≥70% ML bootstrap or ≥0.90 BI posterior probability, the support values are presented near the nodes.
FIGURE 12. Maximum likelihood tree inferred from the COI dataset with 1000 in First record of the order Polyzoniida from the Indian subcontinent with an integrative description of a new genus (Diplopoda, Colobognatha, Siphonotidae)
FIGURE 12. Maximum likelihood tree inferred from the COI dataset with 1000 bootstrap pseudoreplicates implementing the GTR+I+G model. The grey box indicates the polyzoniidan families. The two grey dotted box indicates the clade of the new genus Theratta n. gen. and the tribe Rhinotini. The color of the three newly described polyzoniidan species corresponds to the color in the distribution map. Asterisks (*) indicate the new genus and the three newly described species.
FIGURE 3. Maximum Likelihood tree inferred from a in A new species of Loxosceles Heineken & Lowe, 1832 (Araneae: Sicariidae) from Iranian caves
FIGURE 3. Maximum Likelihood tree inferred from a concatenated matrix of cox1 and rrnL mtDNA and H3 nuDNA gene fragments. Numbers next to nodes correspond to bootstrap support values. L. vonwredei, L. spinulosa, Loxosceles sp., L. speluncarum and L. variegata was used to root the tree. TR = Turkey; IP = Iberian Peninsula; SAR = Sardinia; PT = Portugal; GC = Gran Canaria.
FIGURE 4. Maximum likelihood bootstrap tree for selected cyclostome braconids, using 28S D2-D3 in An enigmatic new genus of Hormiinae (Hymenoptera: Braconidae) from South India
FIGURE 4. Maximum likelihood bootstrap tree for selected cyclostome braconids, using 28S D2-D3 sequence data. Numbers above branches are bootstrap percentages for clades with>50% support. Note that Indohormius gen. nov. is recovered in a clade comprising non-rhyssaline and non-mesostoine taxa with a bootstrap support value of 98%, but its finer level relationships are not significantly supported.
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I in New species of Trichomycterus (Siluriformes: Trichomycteridae) lacking pelvic fins from Paranapanema basin, southeastern Brazil
FIGURE 5. Maximum likelihood tree built with concatenated matrix using cytochrome oxidase sub-united I (COI) and 16S genes, showing the relationships of Trichomycterus pascuali within Trichomycterinae. Numbers on branches of tree denote bootstrap (B) values.
FIGURE 7. Maximum-likelihood tree for 11 in Scolionema sanshin sp. n., a new species (Hydrozoa, Limnomedusae, Olindiidae) from the Ryukyu Archipelago, southern Japan
FIGURE 7. Maximum-likelihood tree for 11 limnomedusan taxa based on the nuclear 18S rDNA data set. Scale bars indicate branch length in substitutions per site. Nodal support values are presented as the ML bootstrap value; only values>50% are shoWn.
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 in A new species of nurse-frog (Aromobatidae, Allobates) from the Madeira River basin with a small geographic range
FIGURE 10. Unrooted maximum likelihood phylogenetic tree reconstructed from a 481 bp fragment of the mitochondrial 16S rDNA sampled from six Allobates bacurau paratypes and other cryptically colored species of Allobates distributed in Brazil and across cis-Andean South America. Clade labels indicate bootstrap support values estimated from 5000 bootstrap replicates (only support values>80% are shown). Basal clades with low bootstrap support should not be considered to reflect the true evolutionary history between taxa. Locations described in parentheses indicate sequence samples obtained from voucher specimens that did not proceed from the species type locality.
FIGURE 1. Maximum likelihood tree inferred from 3221 in A new species of direct-developing frog of the genus Pristimantis (Anura: Terrarana: Craugastoridae) from Cordillera del Cóndor, Ecuador, with comments on threats to the anuran fauna of the region
FIGURE 1. Maximum likelihood tree inferred from 3221 aligned positions of the 16S (2589 aligned bp) and RAG-1 (632 aligned bp) genes depicting the relationships of Pristimantis yantzaza sp. nov.. Bootstrap values are shown above the branches and Bayesian posterior probabilities are shown below except when they are below 50 (bootstrap) or 0.5 (posterior probability). The tree was rooted with Pristimantis versicolor. Museum catalog numbers and locality of origin for vouchers are listed in Table 1.
FIGURE 1. Maximum likelihood tree based the mitochondrial 16S in Molecular systematics of the subgenus Gephyromantis (Phylacomantis) with description of a new subspecies
FIGURE 1. Maximum likelihood tree based the mitochondrial 16S rRNA gene (540 nucleotides, 127 samples) of the subgenus Phylacomantis. The tree was rooted with sequences of Gephyromantis ambohitra (subgenus Asperomantis; not shown). Numbers at nodes are bootstrap proportions in percentage (only shown for values>50%, and not shown for shallow intraspecific nodes).
FIGURE 5. Maximum likelihood phylogenetic tree constructed with UCEs and exon loci dataset for the novel species P in A new species of Plumarella (Octocorallia: Calcaxonia: Primnoidae) from the Northeast Pacific, and the redescription of Plumarella longispina Kinoshita, 1908
FIGURE 5. Maximum likelihood phylogenetic tree constructed with UCEs and exon loci dataset for the novel species P. williamsi (in bold), the redescribed species P. longispina (in red), the related taxa and rooted to outgroup genera. ML bootstrap support values>70% are shown above branches.
FIGURE 1. Maximum Likelihood tree with branch lengths, inferred from a 2,492 in A new species of Hyloscirtus (Anura, Hylidae) from the Colombian and Venezuelan slopes of Sierra de Perijá, and the phylogenetic position of Hyloscirtus jahni (Rivero, 1961)
FIGURE 1. Maximum Likelihood tree with branch lengths, inferred from a 2,492 bp fragment of the mitochondrial genes 12S rRNA, tRNA-Val, and 16S rRNA, depicting phylogenetic relationships of Hyloscirtus species. Bootstrap support values higher than 50% are presented for each node. Values of 100% are represented by an asterisk.
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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.
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.