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242 results for “Maximum Likelihood”
FIGURE 5. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 5. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R. nasuta, based on 2050 bp of mitochondrial DNA (partial cyt b, 12S and 16S genes). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities of 1.0 in Bayesian analyses (no other branches had support values equal to or greater than 0.95). Note the polyphyly of R. melanosterna.
FIGURE 2. Maximum Likelihood tree for cyt b in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 2. Maximum Likelihood tree for cyt b haplotypes (1060 bp) of Rhinoclemmys melanosterna, including sequences of the other eight Rhinoclemmys species. Haplotype codes correspond to Figure 3 and Appendix I (see there for GenBank accession numbers). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities> 0.95 in Bayesian analyses. Root length shortened by 75%. Note the polyphyly of R. melanosterna.
FIGURE 7. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R in Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)
FIGURE 7. Maximum Likelihood tree for Rhinoclemmys melanosterna, R. diademata, R. funerea, R. punctularia and R. nasuta, based on the supermatrix of 2050 bp of mitochondrial DNA (partial cyt b, 12S and 16S genes) concatenated with 3620 bp of nuclear DNA (partial Rag 1, Rag 2, C-mos, R35 and ODC genes). Support values along branches are thorough bootstrap values> 50. Bold branches are supported by posterior probabilities of 1.0 in Bayesian analyses (no other branches had support values equal to or greater than 0.95; for further explanation see text). Root length shortened by 80%. Note the weak support for the monophyly of R. melanosterna and most other clades.
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 dataset rooted according to the result for the COI dataset. Support values are shown as jackknife from parsimony analysis and bootstrap from maximum likelihood respectively separated by /. * indicates 100% values for each support measure.
FIGURE 1. Maximum likelihood tree reconstructed from tef1 in Trichoderma orarium (Hypocreales): a new species from Taiwan
FIGURE 1. Maximum likelihood tree reconstructed from tef1 sequences. The newly described species is displayed in blue bold. We indicated bootstrap values at the nodes based on 1000 replicates only exceeding 50%. Bar scale represents 0.01 substitutions per nucleotide position. T. inhamatum and T. bannaense were used as outgroup. The tef1 sequence accession numbers are provided in parentheses following the strain numbers. "T" denotes type strains.
Code and data for maximum likelihood estimation (MLE) of P. falciparum age from RNA-seq data
<p>The original R code was written by Avi Feller and Jacob Lemieux and is described in this publication:</p> <p>Lemieux JE, Gomez-Escobar N, Feller A, Carret C, Amambua-Ngwa A, Pinches R, Day F, Kyes SA, Conway DJ, Holmes CC and Newbold CI (2009): Statistical estimation of cell-cycle progression and lineage commitment in <em>Plasmodium falciparum </em>reveals a homogeneous pattern of transcription in <em>ex vivo</em> culture. <em>Proc Natl Acad Sci U S A</em> 106(18), 7559-7564 doi: 10.1073/pnas.0811829106 <a href="https://www.pnas.org/doi/full/10.1073/pnas.0811829106">https://www.pnas.org/doi/full/10.1073/pnas.0811829106</a></p> <p>In this deposition, the original R script is adapted for command-line use. For usage instructions, see file "README.md".</p> <p>Furthermore, this deposition contains RNA-seq data for <em>P. falciparum</em> 3D7 cultured with blood from individuals with high, normal or low iron status (experiment 1) or with blood from a healthy donor in the presence vs. absence of 0.7 µM hepcidin (experiment 2) at 6 – 9 and 26 – 29 hours post erythrocyte invasion (hpi). For more details see publication:</p> <p>Iron transport pathways in the human malaria parasite <em>Plasmodium falciparum</em> revealed by RNA-sequencing, Wunderlich et al. (<a href="https://www.biorxiv.org/content/10.1101/2024.04.18.590068v1" target="_blank" rel="noopener">biorxiv</a>).</p> <p>Finally, this deposition contains a variety of pre-processed datasets obtained from the following references:</p> <p>Bártfai R, Hoeijmakers WA, Salcedo-Amaya AM, Smits AH, Janssen-Megens E, Kaan A, Treeck M, Gilberger TW, Françoijs KJ and Stunnenberg HG (2010): H2A.Z demarcates intergenic regions of the <em>Plasmodium falciparum</em> epigenome that are dynamically marked by H3K9ac and H3K4me3. <em>PLoS Pathog</em> 6(12), e1001223 doi: 10.1371/journal.ppat.1001223</p> <p>Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL and Sabeti PC (2015): Strand-specific RNA sequencing in <em>Plasmodium falciparum</em> malaria identifies developmentally regulated long non-coding RNA and circular RNA. <em>BMC Genomics</em> 16(1), 454 doi: 10.1186/s12864-015-1603-4</p> <p>López-Barragán MJ, Lemieux J, Quiñones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K and Su X-z (2011): Directional gene expression and antisense transcripts in sexual and asexual stages of <em>Plasmodium falciparum</em>. <em>BMC Genomics</em> 12(1), 587 doi: 10.1186/1471-2164-12-587</p> <p>Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C and Llinás M (2010): New insights into the blood-stage transcriptome of <em>Plasmodium falciparum</em> using RNA-Seq. <em>Mol Microbiol</em> 76(1), 12-24 doi: 10.1111/j.1365-2958.2009.07026.x</p> <p>Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, Martins RM, Sismeiro O, Coppée JY and Scherf A (2014): Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in <em>Plasmodium falciparum</em>. <em>BMC Genomics</em> 15(1), 150 doi: 10.1186/1471-2164-15-150</p> <p>Wichers JS, Scholz JAM, Strauss J, Witt S, Lill A, Ehnold LI, Neupert N, Liffner B, Lühken R, Petter M, Lorenzen S, Wilson DW, Löw C, Lavazec C, Bruchhaus I, Tannich E, Gilberger TW and Bachmann A (2019): Dissecting the gene expression, localization, membrane topology, and function of the <em>Plasmodium falciparum</em> STEVOR protein family. <em>mBio</em> 10(4), doi: 10.1128/mBio.01500-19</p>
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches. in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on nuclear (ITS) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches.
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches in Hedysarum sunhangii (Fabaceae, Hedysareae), a new species from Pamir-Alay (Babatag Ridge - Uzbekistan)
FIGURE. Bayesian tree based on combined plastid (matK, trnL-trnF) sequence data showing phylogenetic position of Hedysarum sunhangii sp. nov. in Subsect. Crinifera. Bayesian posterior probability (PP) / maximum parsimony (MP) are given on each branch, respectively; maximum likelihood (ML) is below branches
FIGURE. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome. in Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan
FIGURE. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome.
FIGURE 9. Maximum likelihood phylogenetic tree with 100 bootstraps using the aligned 16,409 in Two new species of Rhinogobius (Gobiiformes: Oxudercidae) from Palawan, Philippines, with their phylogenetic placement
FIGURE 9. Maximum likelihood phylogenetic tree with 100 bootstraps using the aligned 16,409 bp of mitochondrial genomes in Rhinogobius including the two new species, R. estrellae and R. tandikan, with Tridentiger kuroiwae as an outgroup taxon. Material sequenced in the present study are shown with the catalogue numbers of the vouchers (beginning with NSMT-P, URM- P, or WPU-PPC-P) and sequences from the International Nucleotide Sequence Database are shown with the accession numbers (R. cliffordpopei, R. duospilus, and R. leavelli). The scale bar indicates 0.02 substitutions per site. Pictures shown along with the species names are of the specimens with an asterisk.
Figure 3. COI–28S concatenated maximum-likelihood tree reconstructed using GARLI 2.0 in Unmasking Aurelia species in the Mediterranean Sea: an integrative morphometric and molecular approach
Figure 3. COI–28S concatenated maximum-likelihood tree reconstructed using GARLI 2.0. Numbers adjacent to nodes show the bootstrap support values. The scale indicates the number of substitutions per site. Reference sequences from GenBank are in bold.
FIGURE 2. Maximum Likelihood tree inferred from a in The Mediterranean species of genus Loxosceles Heineken & Lowe, 1832 (Araneae Sicariidae): Loxosceles imazighen sp. n. from Morocco and first description of the female of L. mrazig Ribera & Planas, 2009 from Tunisia
FIGURE 2. Maximum Likelihood tree inferred from a concatenated dataset of cox1, H3, 16S and 28S gene fragments. Node numbers indicate bootstrap support values. L. vonwredei, L. spinulosa, Loxosceles sp. and L. speluncarum were used to root the tree. CI = Canary Islands; IS = Israel; MA = Morocco; IP = Iberian Peninsula; PT = Portugal; SA = Sardinia; TN = Tunisia; TR= Turkey.
Maximum likelihood parameters for Compton coincidence
<p>Supplemental data to maximum likelihood implementation of Compton coincidence detection encoded in Matlab (https://github.com/KTH-Physics-of-Medical-Imaging/Compton_coincidence)</p>
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE 2. Optimal phylogenetic tree from Maximum Likelihood analyses for the nrITS1–5.8S–ITS2 in Morphology and molecular data of the species of Suillus (Suillaceae, Boletales) associated with Pinus sibirica at the European northeast of Russia
FIGURE 2. Optimal phylogenetic tree from Maximum Likelihood analyses for the nrITS1–5.8S–ITS2 Suillus data. Bootstrap values (BS ≥ 70%) is added to the left of a node as follows: nearest neighbour method / maximum likelihood method. Scale bar indicates expected changes per site. New sequences from the Komi Republic are marked with red blocks. The specimen GenBank accession numbers in parentheses follows the names.
Figure 2. The maximum likelihood tree inferred from 14 594 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 2. The maximum likelihood tree inferred from 14 594 nucleotide sites of 60 Cypriniformes and six outgroups (lnL = -203 966.535). Numbers at each branch indicate the resampling the estimated log likelihood (RELL) local bootstrap probabilities. Asterisks indicate 100% local bootstrap support. Two major clades of Cyprinidae (A and B) correspond with those presented in Cavender & Coburn (1992).
Figure 2. Phylogenetic reconstruction resulting from maximum likelihood analysis using a in Two sea anemones (Cnidaria: Anthozoa: Actiniaria) from the Southern Ocean with evidence of a deep-sea, polar lineage of burrowing sea anemones
Figure 2. Phylogenetic reconstruction resulting from maximum likelihood analysis using a concatenated dataset of three mitochondrial (12S, 16S, COIII) and two nuclear markers (18S, 28S). Coloured boxes indicate actiniarian superfamilies with hypothesized phylogenetic position of Chitinactis marmara and Scytophorus striatus indicated by red stars; clade of burrowing anemones indicated by blue circle. Bootstrap resampling values indicated above branches (ML/MP); only support values> 50% are shown.
FIGURE. Maximum likelihood phylogram of Multiclavula spp. based on ITS sequences. Rooted to Clavulina cristata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap. in New and interesting species of Agaricomycetes from Panama
FIGURE. Maximum likelihood phylogram of Multiclavula spp. based on ITS sequences. Rooted to Clavulina cristata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap.
FIGURE. Maximum likelihood phylogram of Humidicutis spp. based on ITS sequences. Rooted to Humidicutis marginata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap. in New and interesting species of Agaricomycetes from Panama
FIGURE. Maximum likelihood phylogram of Humidicutis spp. based on ITS sequences. Rooted to Humidicutis marginata. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap.
FIGURE 2. Maximum likelihood phylogenetic tree generated from a in Type studies on two Paxillus species (Paxillaceae, Boletales) described from China
FIGURE 2. Maximum likelihood phylogenetic tree generated from a three-locus (nrLSU, ITS, and tef1-α) dataset of the Tricholomopsis species. ML bootstrap (BS>50%) are shown above the branches. Voucher specimens and localities where the specimens were collected are provided. The new combination is in bold.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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