Topiary: Pruning the manual labor from ancestral sequence reconstruction Article Swipe
Kona N. Orlandi
,
Sophia R. Phillips
,
Zachary R. Sailer
,
Joseph Harman
,
Michael J. Harms
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1002/pro.4551
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1002/pro.4551
Ancestral sequence reconstruction (ASR) is a powerful tool to study the evolution of proteins and thus gain deep insight into the relationships among protein sequence, structure, and function. A major barrier to its broad use is the complexity of the task: it requires multiple software packages, complex file manipulations, and expert phylogenetic knowledge. Here we introduce topiary , a software pipeline that aims to overcome this barrier. To use topiary, users prepare a spreadsheet with a handful of sequences. Topiary then: (1) Infers the taxonomic scope for the ASR study and finds relevant sequences by BLAST; (2) Does taxonomically informed sequence quality control and redundancy reduction; (3) Constructs a multiple sequence alignment; (4) Generates a maximum‐likelihood gene tree; (5) Reconciles the gene tree to the species tree; (6) Reconstructs ancestral amino acid sequences; and (7) Determines branch supports. The pipeline returns annotated evolutionary trees, spreadsheets with sequences, and graphical summaries of ancestor quality. This is achieved by integrating modern phylogenetics software (Muscle5, RAxML‐NG, GeneRax, and PastML) with online databases (NCBI and the Open Tree of Life). In this paper, we introduce non‐expert readers to the steps required for ASR, describe the specific design choices made in topiary , provide a detailed protocol for users, and then validate the pipeline using datasets from a broad collection of protein families. Topiary is freely available for download: https://github.com/harmslab/topiary .
Related Topics
Concepts
Computer science
Pruning
Phylogenetic tree
Multiple sequence alignment
Software
Pipeline (software)
Tree (set theory)
Sequence (biology)
Sequence alignment
Data mining
Artificial intelligence
Machine learning
Biology
Gene
Peptide sequence
Programming language
Genetics
Mathematical analysis
Agronomy
Mathematics
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/pro.4551
- OA Status
- green
- Cited By
- 13
- References
- 52
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4312121546
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4312121546Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/pro.4551Digital Object Identifier
- Title
-
Topiary: Pruning the manual labor from ancestral sequence reconstructionWork title
- Type
-
articleOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-12-24Full publication date if available
- Authors
-
Kona N. Orlandi, Sophia R. Phillips, Zachary R. Sailer, Joseph Harman, Michael J. HarmsList of authors in order
- Landing page
-
https://doi.org/10.1002/pro.4551Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.ncbi.nlm.nih.gov/pmc/articles/9847077Direct OA link when available
- Concepts
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Computer science, Pruning, Phylogenetic tree, Multiple sequence alignment, Software, Pipeline (software), Tree (set theory), Sequence (biology), Sequence alignment, Data mining, Artificial intelligence, Machine learning, Biology, Gene, Peptide sequence, Programming language, Genetics, Mathematical analysis, Agronomy, MathematicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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13Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2, 2024: 4, 2023: 5, 2022: 2Per-year citation counts (last 5 years)
- References (count)
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52Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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