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Treffer: Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space.

Title:
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space.
Authors:
Sukumaran J; Biology, San Diego State University, San Diego, CA, USA. jsukumaran@sdsu.edu., Meila M; Statistics, University of Washington, Seattle, 10587, WA, USA.
Source:
BMC bioinformatics [BMC Bioinformatics] 2024 Dec 18; Vol. 25 (1), pp. 385. Date of Electronic Publication: 2024 Dec 18.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: [London] : BioMed Central, 2000-
MeSH Terms:
Software*, Computational Biology/methods ; Information Theory ; Algorithms ; Genetic Speciation ; Phylogeny
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Grant Information:
1937725 Division of Environmental Biology
Contributed Indexing:
Keywords: Distances; Evolutionary biology; Information theory; Metrics; Species delimitation
Entry Date(s):
Date Created: 20241219 Date Completed: 20241219 Latest Revision: 20250104
Update Code:
20250114
PubMed Central ID:
PMC11657818
DOI:
10.1186/s12859-024-05997-y
PMID:
39695946
Database:
MEDLINE

Weitere Informationen

Background: Existing software for comparison of species delimitation models do not provide a (true) metric or distance functions between species delimitation models, nor a way to compare these models in terms of relative clustering differences along a lattice of partitions.
Results: Piikun is a Python package for analyzing and visualizing species delimitation models in an information theoretic framework that, in addition to classic measures of information such as the entropy and mutual information [1], provides for the calculation of the Variation of Information (VI) criterion [2], a true metric or distance function for species delimitation models that is aligned with the lattice of partitions.
Conclusions: Piikun is available under the MIT license from its public repository ( https://github.com/jeetsukumaran/piikun ), and can be installed locally using the Python package manager 'pip'.
(© 2024. The Author(s).)

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: None. Code availability: The source code, documentation, example data sets, etc. are available for download, installation, or direct usage from the Piikun code repository: https://github.com/jeetsukumaran/piikun .