Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space
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...
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BMC
2024-12-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-024-05997-y |
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| author | Jeet Sukumaran Marina Meila |
| author_facet | Jeet Sukumaran Marina Meila |
| author_sort | Jeet Sukumaran |
| collection | DOAJ |
| description | 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‘. |
| format | Article |
| id | doaj-art-711cdba39b144f53a3829eeb6ebae2ee |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-711cdba39b144f53a3829eeb6ebae2ee2024-12-22T12:51:16ZengBMCBMC Bioinformatics1471-21052024-12-0125111110.1186/s12859-024-05997-yPiikun: an information theoretic toolkit for analysis and visualization of species delimitation metric spaceJeet Sukumaran0Marina Meila1Biology, San Diego State UniversityStatistics, University of WashingtonAbstract 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‘.https://doi.org/10.1186/s12859-024-05997-yEvolutionary biologySpecies delimitationInformation theoryMetricsDistances |
| spellingShingle | Jeet Sukumaran Marina Meila Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space BMC Bioinformatics Evolutionary biology Species delimitation Information theory Metrics Distances |
| title | Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space |
| title_full | Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space |
| title_fullStr | Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space |
| title_full_unstemmed | Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space |
| title_short | Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space |
| title_sort | piikun an information theoretic toolkit for analysis and visualization of species delimitation metric space |
| topic | Evolutionary biology Species delimitation Information theory Metrics Distances |
| url | https://doi.org/10.1186/s12859-024-05997-y |
| work_keys_str_mv | AT jeetsukumaran piikunaninformationtheoretictoolkitforanalysisandvisualizationofspeciesdelimitationmetricspace AT marinameila piikunaninformationtheoretictoolkitforanalysisandvisualizationofspeciesdelimitationmetricspace |