{"title":"Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space.","authors":"Jeet Sukumaran, Marina Meila","doi":"10.1186/s12859-024-05997-y","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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'.</p>","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":"25 1","pages":"385"},"PeriodicalIF":2.9000,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12859-024-05997-y","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
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'.
期刊介绍：
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
