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Dataset results
17 results for “Molecular alignment”
Alignments from "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates"
<p>Compressed file containing the alignments at both nucleotide and amino acid level for the manuscript "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates" </p>
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West) in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)
◂Fig. 6 A molecular phylogeny of 56 systematically representative Peridiniaceae, including 42 accessions assignable to P. cinctum from various geographic regions. Maximum likelihood tree (– ln = 21,884.93), as inferred from a rRNA nucleotide alignment (1137 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (CZE Czech Republic, E East, GER Germany, HET Heterocapsaceae, N North, PPE Protoperidiniaceae, POL Poland, rbn ribotype n, S South, SWE Sweden, UKR Ukraine, W West)
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae) in Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy
◂Fig. 4 A molecular tree of 51 systematically representative Peridiniaceae, including all 28 accessions assignable to P. volzii. Maximum Likelihood tree (–ln = 22,017.62), as inferred from a rRNA nucleotide alignment (1,129 parsimony-informative sites) and with strain number information. Numbers on branches are ML bootstrap (above) and Bayesian support values (below) for the clusters (asterisks indicate maximal support values, values under 50 and 0.90, respectively, are not shown). Clades are indicated (abbreviations: HET, Heterocapsaceae; PPE, Protoperidiniaceae)
Towards a rapid sequencing-based molecular surveillance and mosaicism investigation of Toxoplasma gondii (nucleotide alignment dataset)
<p>This dataset includes the nucleotide alignment of eight Toxoplasma gondii genome loci (Sag1 / Chromossome VIII, Gra6 / Chromossome X, PK1 / Chromossome VI, Sag3 / Chromossome XII, L363 / Chromossome VIIb, CB21-4 / Chromossome III, M102 / Chromossome VIIa, Sag2 / Chromossome VIII). Each alignment includes sequences from T. gondii reference strains (retrieved from ToxoDB) as well as sequences from multiple clinical strains (obtained by Sanger / Next-generation sequencing) of the collection of the National Reference Laboratory of Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Portugal. </p>
FIGURE 22 in Corrections to "Padial et al. (2014) Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria"
FIGURE 22. Schematic representation of the new family- and genus-level taxonomy of Brachycephaloidea presented in this study as derived from the results of tree-alignment + parsimony phylogenetic analyses of nucleotide sequences. The placement and affinities of Dischidodactylus and Niceforonia are based on morphological synapomorphies (see text).
Supporting data for "Collisional alignment and molecular rotation control the chemi-ionization of individual conformers of hydroquinone with metastable neon"
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FIGURE 4 in Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
FIGURE 4. Tree-alignment + parsimony: strict consensus of 536 most parsimonious trees of 94413 steps showing relationships among 430 terminals of Brachycephaloidea and 25 outgroup taxa. Dashed branches indicate clades that collapse due to the wildcard Eleutherodactylus dilatus. Numbers above branches are Goodman-Bremer values excluding E. dilatus and those below branches are jackknife percentages excluding (upper) and including (lower) E. dilatus. Linnaean taxa follow previous studies except when otherwise indicated. Non-monophyletic taxa are highlighted in red (monophyletic taxa within paraphyletic groups remain in black).
FIGURE 12 in Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
FIGURE 12. Similarity-alignment + parsimony: strict consensus of 205 most parsimonious trees of 105810 steps for a dataset of 17233 aligned sites of mitochondrial and nuclear DNA showing relationships among 430 terminals of Brachycephaloidea and 25 outgroup taxa. Dashed branches indicate clades that collapse due to the wildcard Eleutherodactylus dilatus. Numbers above branches are Goodman-Bremer values excluding E. dilatus and those below branches are jackknife percentages excluding (upper) and including (lower) E. dilatus; jackknife values reported as a dash (-) were recovered in <5 pseudoreplicates. Non-monophyletic taxa of other authors or differing from the results of our similarity-alignment + parsimony are highlighted in red (monophyletic taxa within paraphyletic groups remain in black).
FIGURE 8 in Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
FIGURE 8. Relationships among families and subfamilies of Brachycephaloidea recognized by Hedges et al. (2008a): (A) similarity-alignment + maximum likelihood of analysis 3 of Hedges et al. (2008a); (B) similarity-alignment + maximum likelihood of the 17-gene analysis of Heinicke et al. (2009); (C) similarity-alignment + maximum likelihood of total evidence analysis of Pyron & Wiens (2011); (D) tree-alignment + parsimony, this study; (E) similarity-alignment + parsimony, this study; (F) similarity-alignment + maximum likelihood, this study. Non-monophyletic taxa are highlighted in red.
Aligned DNA sequence matrix for phylogenetic analyses in the article "Molecular and Morphological Assessment of Rain Frogs in the Pristimantis orestes Species Group (Amphibia: Anura: Strabomantidae) with the Description of Three New Cryptic Species from Southern Ecuador"
<p>The aligned matrix is in fasta format. Genes are arranged as follows:</p> <p>12S = 1–901</p> <p>16S = 902–2094</p> <p>RAG-1 = 2095–2733</p>
Data from: Controlling population of the molecular rotational state and the alignment theoretically by tailored femtosecond laser pulse
We demonstrate that the population of the molecular rotational state through a stimulated impulsive Raman excitation can be controlled by tailoring the femtosecond laser pulse with a V-style phase modulation. The results show that, by precisely manipulating the modulation parameters, both the odd and even populations of the molecular rotational state can be completely suppressed or reconstructed. Meanwhile, the relative excitation between the odd and even populations can be obtained. Finally, we show that field-free molecular alignment can be controlled due to the modulation of the molecular rotational state populations.
Molecular systematics of the tribe Physarieae (Brassicaceae) based on the nuclear ITS, LUMINIDEPENDENS, and chloroplast ndhF: Sequence alignments, trees, and supplemental figures
<p>Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit and chromosomal variation. Building on a previous study of Physarieae based on morphology and <i>ndhF</i> plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and <i>LUMINIDEPENDENS</i> (<i>LD</i>) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous <i>ndh</i>F data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e. DDNLS (<i>Dithyrea</i>, <i>Dimorphocarpa</i>, <i>Nerisyrenia</i>, <i>Lyrocarpa</i>, and <i>Synthlipsis</i>) and PP (<i>Paysonia</i> and <i>Physaria</i>). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly<i> </i>of <i>Dithyrea</i> and the sister relationship of <i>Paysonia</i> to <i>Physaria</i> was consistent in all trees, with the sister relationship of <i>Nerisyrenia </i>to <i>Lyrocarpa </i>supported by <i>ndhF</i> and <i>ITS</i>, and the positions of <i>Dimorphocarpa</i> and <i>Synthlipsis</i> shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by <i>ndhF</i>.</p>
Alignment underpinning the molecular phylogeny of the Streptophyta based on SSU rDNA and rbcL sequence comparisons presented in Figure S1 of the article "Phylogenomic insights into the first multicellular streptophyte"
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Data from: Controlling population of the molecular rotational state and the alignment theoretically by tailored femtosecond laser pulse
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Molecular systematics of the tribe Physarieae (Brassicaceae) based on the nuclear ITS, Luminidependens, and chloroplast ndhF: Sequence alignments, trees, and supplemental figures
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Dataset and Checkpoints of MolEdit: In-silico 3D Molecular Editing through Physics-Informed and Peference-Aligned Generative Foundation Models
<p>This repository hosts the pre-trained checkpoints and data utilized for the development of MolEdit. The corresponding research paper, titled "<em>In-silico</em> 3D Molecular Editing through Physics-Informed and Peference-Aligned Generative Foundation Models" (an early version is preprinted at <a href="doi.org/10.26434/chemrxiv-2023-j2n6l-v2">doi:10.26434/chemrxiv-2023-j2n6l-v2</a>) and the corresponding GitHub repository of <a href="https://github.com/issacAzazel/MolEdit">MolEdit</a> details the application and validation of these checkpoints and data. For further information, please refer to the README.md file contained within this repository.</p>
Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome
GEO Series GSE105211. Homo sapiens. 658 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.