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kde toolbox  (MathWorks Inc)


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    MathWorks Inc kde toolbox
    (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with <t>KDE</t> <t>toolbox</t> to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.
    Kde Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kde toolbox/product/MathWorks Inc
    Average 90 stars, based on 1 article reviews
    kde toolbox - by Bioz Stars, 2026-03
    90/100 stars

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    1) Product Images from "An ancient genome duplication in the speciose reef-building coral genus, Acropora"

    Article Title: An ancient genome duplication in the speciose reef-building coral genus, Acropora

    Journal: bioRxiv

    doi: 10.1101/366435

    (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with KDE toolbox to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.
    Figure Legend Snippet: (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with KDE toolbox to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.

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    (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with <t>KDE</t> <t>toolbox</t> to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.
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    (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with <t>KDE</t> <t>toolbox</t> to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.
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    (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with <t>KDE</t> <t>toolbox</t> to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.
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    (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with KDE toolbox to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.

    Journal: bioRxiv

    Article Title: An ancient genome duplication in the speciose reef-building coral genus, Acropora

    doi: 10.1101/366435

    Figure Lengend Snippet: (a). Frequency distribution of dS values for paralogous gene pairs in five Acropora and one Astreopora species showing that a WGD event occurred in Acropora . Similar peaks (dS value: 0.1-0.3) in dS distributions of five Acropora lineages indicate that a WGD event occurred in Acropora . (Light red: A. digitifera ; Light yellow: A. echinata ; Light green: A. gmmifera ; Light blue: A. subglabra ; Light purple: A. tenuis ; Light cyan: Astreopora sp1). (b). Frequency distribution of dS log values for paralogous genes in Acropora and for orthologous genes showing that a WGD event occurred in the most recent common ancestor of Acropora . Distributions are plotted with a bin size of 0.1. (c). Hypothetical tree topology of duplicated genes in the Acroporidae and the phylogeny of one duplicated gene (alpha-protein kinase 1-like). The phylogenetic tree shows gene retention, loss, and duplications following with WGD. (d). Node age distribution of IAsα. Inferred node ages from 135 phylogenies were analyzed with KDE toolbox to show the peak at 30.78 My, represented by the black solid line. The grey lines represent density estimations from 1000 bootstraps and the black dotted line represents the corresponding 95% confidence interval (27.86 - 34.77 My) from 100 bootstraps.

    Article Snippet: Each distribution was estimated using KDE toolbox in MATLAB, as described previously [ , ].

    Techniques: