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1,199 results for “Alignement”
intraspecific the to correspond. outgroups bold: grey in in Values; retzii. ) pb Microphis 605 ( : alignment red in; . I nov . subunit sp oxydase arrakisae c Microphis cytochrome: blue the in; on torrentius based) Microphis p-distances: green uncorrected in; (nicoleae matrix distance Microphis : Pairwise yellow In. . 2 divergence TABLE in A new freshwater pipefish species (Syngnathidae: Microphis) from the Sunda shelf islands, Indonesia
intraspecific the to correspond. outgroups bold: grey in in Values; retzii. ) pb Microphis 605 ( : alignment red in; . I nov . subunit sp oxydase arrakisae c Microphis cytochrome: blue the in; on torrentius based) Microphis p-distances: green uncorrected in; (nicoleae matrix distance Microphis : Pairwise yellow In. . 2 divergence TABLE
Resupinatus ITS and LSU concatenated alignment
<p><span>ITS1+ITS2: 1–300</span></p> <p><span>LSU: 301–1193</span></p>
GAPS (Guitar-Aligned Performance Scores) Dataset
<p>Release of the aligned MIDI transcriptions, scores and downbeats that constitute the GAPS dataset. Links to YouTube URLs for audio and video are provided in the accompanying metadata file. See below for the abstract of the publication.</p> <p>Abstract:</p> <p>We introduce GAPS (Guitar-Aligned Performance Scores), a new dataset of classical guitar performances, and a benchmark guitar transcription model that achieves state-of-the-art performance on GuitarSet in both supervised and zero-shot settings. GAPS is the largest dataset of real guitar audio, containing 14 hours of freely available audio-score aligned pairs, recorded in diverse conditions by over 200 performers, together with high-resolution note-level MIDI alignments and performance videos. These enable us to train a state-of-the-art model for automatic transcription of solo guitar recordings which can generalise well to real world audio that is unseen during training.</p>
Data from: Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets
The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long been considered the most rigorous technique for estimating alignments and trees, but little is known about the accuracy of such methods on biological benchmarks. We report the results of an extensive study evaluating the most popular protein alignment methods as well as the statistical co-estimation method BAli-Phy on 1192 protein data sets from established benchmarks as well as on 120 simulated data sets. Our study (which used more than 230 CPU years for the BAli-Phy analyses alone) shows that BAli-Phy has better precision and recall (with respect to the true alignments) than the other alignment methods on the simulated data sets, but has consistently lower recall on the biological benchmarks (with respect to the reference alignments) than many of the other methods. In other words, we find that BAli-Phy systematically under-aligns when operating on biological sequence data, but shows no sign of this on simulated data. There are several potential causes for this change in performance, including model misspecification, errors in the reference alignments, and conflicts between structural alignment and evolutionary alignments, and future research is needed to determine the most likely explanation. We conclude with a discussion of the potential ramifications for each of these possibilities.
Data from: Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments
This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O'Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O'Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O'Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O'Brien & Wibmer (1982) was comprised solely of P. griseus Sleeper, 1960 sec. O'Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: M. bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., M. aeriballux [JF2015], sp. n., M. cracens [JF2015], sp. n., M. gravivultus [JF2015], sp. n., M. imberbus [JF2015], sp. n., M. reburrus [JF2015], sp. n., M. politus [JF2015], sp. n., M. puticulatus [JF2015], sp. n., M. rutellirostris [JF2015], sp. n., and M. trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places P. griseus sec. O'Brien & Wibmer (1982) within the genus as sister to M. rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of Minyomerus [JF2015], and its sole member P. griseus sec. Sleeper (1960) is moved to Minyomerus [JF2015] as M. griseus [JF2015], comb. n. In addition, the formerly designated type M. innocuus Horn, 1876 sec. Pierce (1913), syn. n. is changed to junior synonymy of M. microps (Say, 1831) [JF2015] which has priority. The genus is widespread throughout western North America, ranging from Canada to Mexico and Baja California. Apparent patterns of interspecific diversity of exterior and genitalic morphology, varying host plant ranges, overlapping and widely extending species distributions, suggest an early origin for Minyomerus [JF2015], with a diversification that likely followed the development of North American desert biomes. Three species in the genus – i.e., M. languidus Horn, 1876 [JF2015], M. microps [JF2015], and M. trisetosus [JF2015] – are putatively considered parthenogenetic.
Sample data for sequencing reads alignment
<p>These data are used for learning sequencing reads alignment and cluster usage</p>
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 sequences were obtained from sanguinicolids of different host/location combinations (not differentiated by morphological comparisons) only one representative sequence has been included here. Gaps of five spaces delineate the 5' and 3' ends of ITS2 (and subsequent 3' end of 5.8S and the 5' end of 28S).
FIGURE 1. ITS2 sequence alignment for threadlike sanguinicolids. Where identical ITS2 in An exceptionally rich complex of Sanguinicolidae von Graff, 1907 (Platyhelminthes: Trematoda) from Siganidae, Labridae and Mullidae (Teleostei: Perciformes) from the Indo-west Pacific Region
FIGURE 1. ITS2 sequence alignment for threadlike sanguinicolids. Where identical ITS2 sequences were obtained for sanguinicolids from different host/location combinations only one sequence has been included here. Gaps of five spaces delineate the 5' and 3' ends of ITS2 (and subsequent 3' end of 5.8S and the 5' end of 28S).
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.
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution
<p>Datasets related to "TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution."</p>
Figure 17 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 17. Summary of recovery of selected basal and Pimpliformes clades as monophyletic in most parsimonious trees from analysis of combined morphological and CLUSTAL-aligned molecular data showing effects of different gap-opening and gap-extension values and treatment of gaps as informative or uninformative. Groups are coloured if they were recovered in any of the most parsimonious trees obtained from a particular combination of parameters.
Figure 21 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 21. Strict consensus most parsimonious tree of analysis of elided molecular data set (with gaps treated as missing data) combined with morphological data up-weighted 444 times to give equivalent total clade support (length 1,823,755; RI 0.888). Coloured bars indicate current subfamily classification.
Figure 11 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 11. Chitinous venom gland and reservoir intimas. (A) Schizopyga sp. (Pimplinae); (B) Perithous sp. (Pimplinae); (C) Delomerista sp. (Pimplinae); (D) Pseudorhyssa alpestris (Poemeniinae); (E) Rhyssa persuasoria (L.) (Rhyssinae); (F) Exeristes sp. (Pimplinae); (G) Clasis sp. (Claseinae).
Figure 22 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 22. Strict consensus most parsimonious tree of analysis of elided molecular data set (with gaps treated as informative) combined with morphological data up-weighted 483 times to give equivalent total clade support (length 2,360,406; RI 0.871). Coloured bars indicate current subfamily classification.
Figure 14 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 14. Chitinous venom gland and reservoir intimas: (A) Banchus sp. (Banchinae); (B) Erythrodolius griffithsorum Gauld (Phrudinae); (C) Hellwigia elegans Gravenhorst (Ophioninae); (D) Ophion sp. (Ophioninae); (E) Stilbops vetula (Gravenhorst) (Stilbopinae); (F) Tersilochus sp. (Tersilochinae); (G) Mesochorus sp. (Mesochorinae); (H) unmacerated venom gland and reservoir of Hybrizon sp. (Hybrizontinae).
Figure 6 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 6. Light photomicrographs of upper ovipositor valve bases following maceration in KOH (aq.) and light staining with chlorazol black. (A) Phytodietus (Tryphoninae); (B) Westwoodia (Ctenopelmatini); (C) Oxytorus (Oxytorinae); (D) Hybrizon (Hybrizontinae).
Figure 8 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 8. Drawings of transverse sections through mid-part of ovipositor valves. (A) Apophua sp. (Banchinae); (B) Euryproctus sp. (Ctenopelmatinae); (C) Trematopygus sp. (Ctenopelmatinae); (D) Alexeter sp. (Ctenopelmatinae); (E) Lamachus eques (Hartig) (Ctenopelmatinae); (F) Hadrodactylus sp. (Ctenopelmatinae); (G) Skiapus sp. (Ophioninae); (H) Enicospilus kauaiensis (Ashmead), upper valve only (Ophioninae); (I) Scolobates sp., lower valve only (Ctenopelmatinae).
Figure 5 in A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision
Figure 5. Light photomicrographs of upper ovipositor valve bases following maceration in KOH (aq.) and light staining with chlorazol black. (A) Netelia (Tryphoninae: Phytodietini); (B) Metopius (Metopiinae); (C) Lissonota (Banchinae: Atrophini); (D) Astiphromma (Mesochorinae); (E) Gravenhorstia picta Boie (Anomaloninae); (F) Dusona (Campopleginae).
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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.