PhyKIT: A Multitool for Phylogenomics
Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for div...
| Autores: | , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
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| Acceso en línea: | http://hdl.handle.net/10261/373344 https://api.elsevier.com/content/abstract/scopus_id/85208116627 |
| Access Level: | acceso abierto |
| Palabra clave: | Software tools Comparative genomics Genomics Phylogenomics Phylogeny Sequence alignments |
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PhyKIT: A Multitool for Phylogenomics |
| title |
PhyKIT: A Multitool for Phylogenomics |
| spellingShingle |
PhyKIT: A Multitool for Phylogenomics Steenwyk, Jacob L. Software tools Comparative genomics Genomics Phylogenomics Phylogeny Sequence alignments |
| title_short |
PhyKIT: A Multitool for Phylogenomics |
| title_full |
PhyKIT: A Multitool for Phylogenomics |
| title_fullStr |
PhyKIT: A Multitool for Phylogenomics |
| title_full_unstemmed |
PhyKIT: A Multitool for Phylogenomics |
| title_sort |
PhyKIT: A Multitool for Phylogenomics |
| dc.creator.none.fl_str_mv |
Steenwyk, Jacob L. Martínez-Redondo, Gemma Isabel Buida, Thomas J. Gluck-Thaler, Emile Shen, Xing-Xing Gabaldón, Toni Rokas, Antonis Fernández García, Rosa María |
| author |
Steenwyk, Jacob L. |
| author_facet |
Steenwyk, Jacob L. Martínez-Redondo, Gemma Isabel Buida, Thomas J. Gluck-Thaler, Emile Shen, Xing-Xing Gabaldón, Toni Rokas, Antonis Fernández García, Rosa María |
| author_role |
author |
| author2 |
Martínez-Redondo, Gemma Isabel Buida, Thomas J. Gluck-Thaler, Emile Shen, Xing-Xing Gabaldón, Toni Rokas, Antonis Fernández García, Rosa María |
| author2_role |
author author author author author author author |
| dc.contributor.none.fl_str_mv |
Howard Hughes Medical Institute National Science Foundation (US) National Institutes of Health (US) National Institute of Allergy and Infectious Diseases (US) Burroughs Wellcome Fund National Natural Science Foundation of China Generalitat de Catalunya Ministerio de Ciencia e Innovación (España) Agencia Estatal de Investigación (España) European Research Council Agència de Gestió d'Ajuts Universitaris i de Recerca Steenwyk, Jacob L. [0000-0002-8436-595X] Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
Software tools Comparative genomics Genomics Phylogenomics Phylogeny Sequence alignments |
| topic |
Software tools Comparative genomics Genomics Phylogenomics Phylogeny Sequence alignments |
| description |
Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing-such as renaming FASTA entries or tree tips-are also discussed. These protocols demonstrate how simple command-line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gaining clues about gene function. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Installing PhyKIT and syntax for usage Basic Protocol 2: Constructing a phylogenomic supermatrix Basic Protocol 3: Detecting anomalies in orthology relationships Basic Protocol 4: Quantifying biases in phylogenomic data matrices and related measures Basic Protocol 5: Identifying polytomies Basic Protocol 6: Assessing gene-gene coevolution as a genetic screen. |
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2024 |
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2024 2024 2024 |
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http://hdl.handle.net/10261/373344 https://api.elsevier.com/content/abstract/scopus_id/85208116627 |
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http://hdl.handle.net/10261/373344 https://api.elsevier.com/content/abstract/scopus_id/85208116627 |
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John Wiley & Sons |
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John Wiley & Sons |
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PhyKIT: A Multitool for PhylogenomicsSteenwyk, Jacob L.Martínez-Redondo, Gemma IsabelBuida, Thomas J.Gluck-Thaler, EmileShen, Xing-XingGabaldón, ToniRokas, AntonisFernández García, Rosa MaríaSoftware toolsComparative genomicsGenomicsPhylogenomicsPhylogenySequence alignmentsMultiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing-such as renaming FASTA entries or tree tips-are also discussed. These protocols demonstrate how simple command-line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gaining clues about gene function. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Installing PhyKIT and syntax for usage Basic Protocol 2: Constructing a phylogenomic supermatrix Basic Protocol 3: Detecting anomalies in orthology relationships Basic Protocol 4: Quantifying biases in phylogenomic data matrices and related measures Basic Protocol 5: Identifying polytomies Basic Protocol 6: Assessing gene-gene coevolution as a genetic screen.JLS is a Howard Hughes Medical Institute Awardee of the Life Sciences Research Foundation. Research in AR's lab is supported by grants from the US National Science Foundation (DEB-2110404), the US National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01 AI153356), and the Burroughs Wellcome Fund. GIMR acknowledges the support of the Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya and ESF Investing in your future (grant 2021 FI_B 00476). X-XS was supported by the National Key R&D Program of China (2022YFD1401600) and the National Science Foundation for Distinguished Young Scholars of Zhejiang Province (LR23C140001). RF acknowledges support from the following sources of funding: Ramón y Cajal fellowship (grant agreement no. RYC2017-22492 funded by MCIN/AEI /10.13039/501100011033 and ESF ‘Investing in your future’), the European Research Council (this project has received funding from the European Research Council [ERC] under the European's Union's Horizon 2020 research and innovation programme, grant agreement no. 948281) and the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya (AGAUR 2021-SGR00420).Peer reviewedJohn Wiley & SonsHoward Hughes Medical InstituteNational Science Foundation (US)National Institutes of Health (US)National Institute of Allergy and Infectious Diseases (US)Burroughs Wellcome FundNational Natural Science Foundation of ChinaGeneralitat de CatalunyaMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)European Research CouncilAgència de Gestió d'Ajuts Universitaris i de RecercaSteenwyk, Jacob L. [0000-0002-8436-595X]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/373344https://api.elsevier.com/content/abstract/scopus_id/85208116627reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI//RYC2017-22492info:eu-repo/grantAgreement/EC/H2020/948281https://doi.org/10.1002/cpz1.70016Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3733442026-05-22T06:33:51Z |
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