Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree Article Swipe
Meijun Chen
,
Xiao Luo
,
Shuangbin Xu
,
Lin Li
,
Junrui Li
,
Zijing Xie
,
Qianwen Wang
,
Yufan Liao
,
Bingdong Liu
,
Wenquan Liang
,
Ke Mo
,
Qiong Song
,
Xia Chen
,
Tommy Tsan‐Yuk Lam
,
Guangchuang Yu
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1002/imt2.269
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1002/imt2.269
In metabarcoding research, such as taxon identification, phylogenetic placement plays a critical role. However, many existing phylogenetic placement methods lack comprehensive features for downstream analysis and visualization. Visualization tools often ignore placement uncertainty, making it difficult to explore and interpret placement data effectively. To overcome these limitations, we introduce a scalable approach using treeio and ggtree for parsing and visualizing phylogenetic placement data. The treeio ‐ ggtree method supports placement filtration, uncertainty exploration, and customized visualization. It enhances scalability for large analyses by enabling users to extract subtrees from the full reference tree, focusing on specific samples within a clade. Additionally, this approach provides a clearer representation of phylogenetic placement uncertainty by visualizing associated placement information on the final placement tree.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/imt2.269
- OA Status
- gold
- Cited By
- 2
- References
- 27
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4406295062
All OpenAlex metadata
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https://openalex.org/W4406295062Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/imt2.269Digital Object Identifier
- Title
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Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtreeWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-01-12Full publication date if available
- Authors
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Meijun Chen, Xiao Luo, Shuangbin Xu, Lin Li, Junrui Li, Zijing Xie, Qianwen Wang, Yufan Liao, Bingdong Liu, Wenquan Liang, Ke Mo, Qiong Song, Xia Chen, Tommy Tsan‐Yuk Lam, Guangchuang YuList of authors in order
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https://doi.org/10.1002/imt2.269Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
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https://doi.org/10.1002/imt2.269Direct OA link when available
- Concepts
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Visualization, Phylogenetic tree, Computer science, Scalability, Tree (set theory), Identification (biology), Data mining, Data visualization, Clade, Parsing, Data science, Artificial intelligence, Biology, Database, Mathematics, Ecology, Biochemistry, Mathematical analysis, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
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2Total citation count in OpenAlex
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2025: 2Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.analyses | 82 |
| abstract_inverted_index.analysis | 25 |
| abstract_inverted_index.approach | 52, 103 |
| abstract_inverted_index.critical | 12 |
| abstract_inverted_index.enabling | 84 |
| abstract_inverted_index.enhances | 78 |
| abstract_inverted_index.existing | 16 |
| abstract_inverted_index.features | 22 |
| abstract_inverted_index.focusing | 94 |
| abstract_inverted_index.overcome | 45 |
| abstract_inverted_index.provides | 104 |
| abstract_inverted_index.scalable | 51 |
| abstract_inverted_index.specific | 96 |
| abstract_inverted_index.subtrees | 88 |
| abstract_inverted_index.supports | 69 |
| abstract_inverted_index.difficult | 36 |
| abstract_inverted_index.interpret | 40 |
| abstract_inverted_index.introduce | 49 |
| abstract_inverted_index.placement | 9, 18, 32, 41, 62, 70, 110, 115, 120 |
| abstract_inverted_index.reference | 92 |
| abstract_inverted_index.research, | 3 |
| abstract_inverted_index.associated | 114 |
| abstract_inverted_index.customized | 75 |
| abstract_inverted_index.downstream | 24 |
| abstract_inverted_index.filtration, | 71 |
| abstract_inverted_index.information | 116 |
| abstract_inverted_index.scalability | 79 |
| abstract_inverted_index.uncertainty | 72, 111 |
| abstract_inverted_index.visualizing | 60, 113 |
| abstract_inverted_index.effectively. | 43 |
| abstract_inverted_index.exploration, | 73 |
| abstract_inverted_index.limitations, | 47 |
| abstract_inverted_index.phylogenetic | 8, 17, 61, 109 |
| abstract_inverted_index.uncertainty, | 33 |
| abstract_inverted_index.Additionally, | 101 |
| abstract_inverted_index.Visualization | 28 |
| abstract_inverted_index.comprehensive | 21 |
| abstract_inverted_index.metabarcoding | 2 |
| abstract_inverted_index.representation | 107 |
| abstract_inverted_index.visualization. | 27, 76 |
| abstract_inverted_index.identification, | 7 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 95 |
| corresponding_author_ids | https://openalex.org/A5027320896, https://openalex.org/A5033703745, https://openalex.org/A5100423108 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 15 |
| corresponding_institution_ids | https://openalex.org/I109935558, https://openalex.org/I2800906782, https://openalex.org/I4387155976, https://openalex.org/I58200834, https://openalex.org/I889458895 |
| citation_normalized_percentile.value | 0.86216986 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |