Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies
As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, ‘Phylobook’ was developed. Starting with a sequence alignment file...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2024-06-01
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| Series: | BioTechniques |
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| Online Access: | https://www.tandfonline.com/doi/10.2144/btn-2023-0056 |
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| author | Jeffrey C Furlong Peter D Darley Wenjie Deng James I Mullins Roger E Bumgarner |
| author_facet | Jeffrey C Furlong Peter D Darley Wenjie Deng James I Mullins Roger E Bumgarner |
| author_sort | Jeffrey C Furlong |
| collection | DOAJ |
| description | As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, ‘Phylobook’ was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. Accurate lineage assignment, which is difficult to automate, is aided using annotations created by different clustering methods. Phylobook provides web-based display combined with automated clustering and manual editing to allow for expert assessment and correction of lineage assignments and extraction for downstream analysis. |
| format | Article |
| id | doaj-art-92110fb6fadc4b438da9f0c5e3707ea8 |
| institution | Kabale University |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2024-06-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-92110fb6fadc4b438da9f0c5e3707ea82025-01-16T15:38:48ZengTaylor & Francis GroupBioTechniques0736-62051940-98182024-06-0176626327410.2144/btn-2023-0056Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogeniesJeffrey C Furlong0Peter D Darley1Wenjie Deng2James I Mullins3Roger E Bumgarner4Department of Microbiology, University of Washington School of Medicine, Box 358070, WA 98195-8070, USADepartment of Microbiology, University of Washington School of Medicine, Box 358070, WA 98195-8070, USADepartment of Microbiology, University of Washington School of Medicine, Box 358070, WA 98195-8070, USADepartment of Microbiology, University of Washington School of Medicine, Box 358070, WA 98195-8070, USADepartment of Microbiology, University of Washington School of Medicine, Box 358070, WA 98195-8070, USAAs the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, ‘Phylobook’ was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. Accurate lineage assignment, which is difficult to automate, is aided using annotations created by different clustering methods. Phylobook provides web-based display combined with automated clustering and manual editing to allow for expert assessment and correction of lineage assignments and extraction for downstream analysis.https://www.tandfonline.com/doi/10.2144/btn-2023-0056highlighter plotlineage assignmentphylogenysequence annotationsequence extraction |
| spellingShingle | Jeffrey C Furlong Peter D Darley Wenjie Deng James I Mullins Roger E Bumgarner Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies BioTechniques highlighter plot lineage assignment phylogeny sequence annotation sequence extraction |
| title | Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies |
| title_full | Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies |
| title_fullStr | Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies |
| title_full_unstemmed | Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies |
| title_short | Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies |
| title_sort | phylobook a tool for display clade annotation and extraction of sequences from molecular phylogenies |
| topic | highlighter plot lineage assignment phylogeny sequence annotation sequence extraction |
| url | https://www.tandfonline.com/doi/10.2144/btn-2023-0056 |
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