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34 results for “maximum likelihood phylogeny”
URL list for downloading 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 is a list of Zenodo URL pointers to a dataset 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>
Fig. 79. Maximum likelihood phylogeny inferred with IQTREE ver. 2.1.2 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Fig. 79. Maximum likelihood phylogeny inferred with IQTREE ver. 2.1.2. The major clades found in Prebus (2017) are highlighted, and the focal species of the current study (all within the 'Palearctic clade IV') are evidenced as in Figs 75–78. Maximum likelihood bootstrap support for all nodes are 100, except where indicated.
Fig. 4. Maximum likelihood tree for 43 in Molecular phylogeny of Indonesian Lymantria Tussock Moths (Lepidoptera: Erebidae) based on CO I gene sequences
Fig. 4. Maximum likelihood tree for 43 species of Lymantria based all substitutions of CO I gene (Bootstrap support are shown at the nodes; ID=specimens from Indonesia).
◂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. 5. Maximum likelihood tree for 10 in Molecular phylogeny of Indonesian Zeuzera (Lepidoptera: Cossidae) wood borer moths based on CO I gene sequence
Fig. 5. Maximum likelihood tree for 10 species of Zeuzera based on all substitution of CO I gene (Bootstrap support are shown ath the nodes).
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to the number of expected nucleotide substitutions per site.
Fig. 3. Maximum likelihood phylogeny from 882 in A fresh start in ambersnail (Gastropoda: Succineidae) taxonomy: finding a foothold using a widespread species of Oxyloma
Fig. 3. Maximum likelihood phylogeny from 882 bp alignment of 15 LSU sequences presenting only the focal taxa and localities. Ultra-fast bootstrap values indicated behind the nodes supported. Full 51-individual analysis reported in Supp. file 2, Supp. file 3. Type localities indicated with an *.
Fig. 2. Maximum likelihood phylogeny from 690 in A fresh start in ambersnail (Gastropoda: Succineidae) taxonomy: finding a foothold using a widespread species of Oxyloma
Fig. 2. Maximum likelihood phylogeny from 690 bp alignment of 34 COI sequences presenting only the focal taxa and localities. Ultra-fast bootstrap values indicated behind the nodes supported. Full 142-individual analysis reported in Supp. file 2, Supp. file 3. Type localities indicated with an *. Species supported by species delimitation analyses indicated with a hollow circle.
Figure 10. Maximum likelihood tree estimated using Garli 2.0 with 5 in Systematics and Phylogeny of the Australian Cicada Genus Pauropsalta Goding and Froggatt, 1904 and Allied Genera (Hemiptera: Cicadidae: Cicadettini)
Figure 10. Maximum likelihood tree estimated using Garli 2.0 with 5 loci (1 mtDNA and 4 nDNA). Branch support values are bootstrap percentages from 100 non parametric bootstrap replicates. Bootstrap support values ≥ 70 are shown. Molecular voucher numbers are adjacent to species names.
FIG. 4. Maximum-likelihood phylogeny for 45 in Phylogenetic Relationships of New World Porcupines (Rodentia, Erethizontidae): Implications for Taxonomy, Morphological Evolution, and Biogeography
FIG. 4. Maximum-likelihood phylogeny for 45 ingroup (erethizontid) terminals; outgroup taxa are not shown. Labeling conventions and nodal support statistics are the same as in figure 3. Capital letters (A, B, C) indicate unnamed clades discussed in the text.
CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
<p>This folder includes simulated and real data used in validating CNETML, a new maximum likelihood method designed to reconstruct the evolutionary history of multiple samples of a single patient which may be taken at different locations and/or times, which can take as input (relative) total integer copy numbers called from shallow whole genome sequencing data.</p>
Fig. 1. Phylogeny and habitus shots. A. Maximum Likelihood phylogeny for the genus Aname L. Koch, 1873 in Description of five new Aname L. Koch, 1873 (Araneae, Anamidae) species collected on Bush Blitz expeditions
Fig. 1. Phylogeny and habitus shots. A. Maximum Likelihood phylogeny for the genus Aname L. Koch, 1873 showing major clades and the position of new species described herein (blue taxa), support values on the phylogeny show the results of 1000 ultrafast bootstrap replicates: black circles = ≥ 95%; grey circles = 80–94%; support values less than 80% are written. Support values for some very shallow intraspecific nodes have been removed for clarity. Photos on the right (by M. Harvey) show: B. Aname ningaloo sp. nov. ♀ (WAM T148012). C. Aname salina sp. nov. ♀ (WAM T148135). D. A. salina sp. nov. ♂ (WAM T153270).
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
Online phylogenetics using parsimony produces slightly better trees and is dramatically more efficient for large SARS-CoV-2 phylogenies than de novo and maximum-likelihood approaches
Open the record for dataset details and reuse information.
FIGURE 8. Maximum likelihood tree showing the relationships among partial cytochrome b in Geographic variation, phylogeny and systematic status of Gracilinanus microtarsus (Mammalia: Didelphimorphia: Didelphidae)
FIGURE 8. Maximum likelihood tree showing the relationships among partial cytochrome b sequences of Gracilinanus spp. Bootstrap support and Bayesian posterior probabilities based on molecular dataset are provided above each branch. Bayesian posterior probabilities based on the combined (morphological + molecular) dataset is provided below each branch. The numbers beside the localities correspond to the same numbers shown on the map (Figure 11). The symbols represent: (●) "small microtarsus", (․) "large microtarsus" and (˔) "ehrhardti".
FIGURE 17. Maximum likelihood tree built with the GTR correction with 1190 in Taxonomy and phylogeny of calcareous sponges (Porifera: Calcarea: Calcinea) from Brazilian mid-shelf and oceanic islands
FIGURE 17. Maximum likelihood tree built with the GTR correction with 1190 bp of the nuclear ITS marker. Bootstrap values are given on the branches. Names in bold are of the described species. Sequences obtained in the present study are marked with an asterisk.
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.
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 4. Best maximum likelihood phylogenies, A in On the origin and systematic position of the Azorean goldenrod, Solidago azorica (Asteraceae)
FIGURE 4. Best maximum likelihood phylogenies, A—based on the combined nuclear ribosomal ETS and ITS regions (1134 basepairs); B—based on the plastid trnQ-rps16 and trnH-psbA regions (1410 basepairs). Likelihood bootstrap values>60 shown at the nodes. Solidago azorica highlighted in red, S. sempervirens in green; GB-sequence downloaded from GenBank.
FIGURE 4. Maximum likelihood tree showing the seven Moraceae tribes. Unlabeled nodes had 100 in Delimitation of the new tribe Parartocarpeae (Moraceae) is supported by a 333- gene phylogeny and resolves tribal level Moraceae taxonomy
FIGURE 4. Maximum likelihood tree showing the seven Moraceae tribes. Unlabeled nodes had 100% bootstrap support in both analyses. Labeled nodes show support from maximum likelihood analysis, with support from the ASTRAL species tree reconciliation in parentheses.
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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.