TreeDist (Q60639): Difference between revisions
From MaRDI portal
Removed claim: imports (P585): phangorn (Q20321) |
Added link to MaRDI item. |
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Property / last update: 1 May 2023 / rank | |||||||||||||||
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Property / imports: Rdpack / rank | |||||||||||||||
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Property / imports: shiny / rank | |||||||||||||||
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Property / imports: shinyjs / rank | |||||||||||||||
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Property / imports: TreeTools / rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees / rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: The Generalized Robinson-Foulds Metric / rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: A novel algorithm and web-based tool for comparing two alternative phylogenetic trees / rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Matching Split Distance for Unrooted Binary Phylogenetic Trees / rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution / rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Some notes on the nearest neighbour interchange distance / rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Robust Analysis of Phylogenetic Tree Space / rank | |||||||||||||||
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1.0.0 | |||||||||||||||
Property / software version identifier: 1.0.0 / rank | |||||||||||||||
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publication date: 30 June 2020
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1.1.1 | |||||||||||||||
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publication date: 10 July 2020
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publication date: 28 August 2020
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publication date: 17 September 2020
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publication date: 20 January 2021
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2.0.2 | |||||||||||||||
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publication date: 27 January 2021
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publication date: 31 January 2021
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2.1.0 | |||||||||||||||
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publication date: 12 July 2021
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2.1.1 | |||||||||||||||
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publication date: 13 July 2021
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2.2.0 | |||||||||||||||
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publication date: 13 September 2021
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2.3.0 | |||||||||||||||
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publication date: 4 January 2022
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publication date: 23 March 2022
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publication date: 20 July 2022
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2.5.0 | |||||||||||||||
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publication date: 7 October 2022
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2.6.2 | |||||||||||||||
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publication date: 30 June 2023
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publication date: 25 August 2023
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2.7.0 | |||||||||||||||
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publication date: 25 October 2023
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25 October 2023
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Property / last update: 25 October 2023 / rank | |||||||||||||||
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Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for calculating the median of sets of trees, and for computing the information content of trees and splits. | |||||||||||||||
Property / description: Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for calculating the median of sets of trees, and for computing the information content of trees and splits. / rank | |||||||||||||||
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Property / author | |||||||||||||||
Property / author: Martin R. Smith / rank | |||||||||||||||
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Property / copyright license: GNU General Public License / rank | |||||||||||||||
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Property / copyright license: GNU General Public License / qualifier | |||||||||||||||
edition/version: ≥ 3 (English) | |||||||||||||||
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Property / depends on software: stats / rank | |||||||||||||||
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Property / depends on software: R / rank | |||||||||||||||
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software version identifier: ≥ 3.4.0 | |||||||||||||||
Property / imports | |||||||||||||||
Property / imports: ape / rank | |||||||||||||||
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software version identifier: ≥ 5.0 | |||||||||||||||
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Property / imports: cli / rank | |||||||||||||||
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software version identifier: ≥ 3.0 | |||||||||||||||
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Property / imports: colorspace / rank | |||||||||||||||
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Property / imports: memoise / rank | |||||||||||||||
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Property / imports: phangorn / rank | |||||||||||||||
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Property / imports: phangorn / qualifier | |||||||||||||||
software version identifier: ≥ 2.2.1 | |||||||||||||||
Property / imports | |||||||||||||||
Property / imports: Rdpack / rank | |||||||||||||||
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Property / imports: Rdpack / qualifier | |||||||||||||||
software version identifier: ≥ 0.7 | |||||||||||||||
Property / imports | |||||||||||||||
Property / imports: shiny / rank | |||||||||||||||
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Property / imports: shinyjs / rank | |||||||||||||||
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Property / imports | |||||||||||||||
Property / imports: TreeTools / rank | |||||||||||||||
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Property / imports: TreeTools / qualifier | |||||||||||||||
software version identifier: ≥ 1.7.2 | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees / rank | |||||||||||||||
Normal rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: The Generalized Robinson-Foulds Metric / rank | |||||||||||||||
Normal rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: A novel algorithm and web-based tool for comparing two alternative phylogenetic trees / rank | |||||||||||||||
Normal rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Matching Split Distance for Unrooted Binary Phylogenetic Trees / rank | |||||||||||||||
Normal rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution / rank | |||||||||||||||
Normal rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Some notes on the nearest neighbour interchange distance / rank | |||||||||||||||
Normal rank | |||||||||||||||
Property / cites work | |||||||||||||||
Property / cites work: Robust Analysis of Phylogenetic Tree Space / rank | |||||||||||||||
Normal rank | |||||||||||||||
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Property / MaRDI profile type: MaRDI software profile / rank | |||||||||||||||
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links / mardi / name | links / mardi / name | ||||||||||||||
Latest revision as of 19:56, 12 March 2024
Calculate and Map Distances Between Phylogenetic Trees
Language | Label | Description | Also known as |
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English | TreeDist |
Calculate and Map Distances Between Phylogenetic Trees |
Statements
25 October 2023
0 references
Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for calculating the median of sets of trees, and for computing the information content of trees and splits.
0 references
0 references