ArticleBMC evolutionary biology2020
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly.
Article in BMC evolutionary biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
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- Phylogenomics of the rarest animals: a second species of Micrognathozoa identified by machine learning.Proceedings. Biological sciences · 2025Article
- Investigating the Impact of Whole-Genome Duplication on Transposable Element Evolution in Teleost Fishes.Genome biology and evolution · 2025Article
- Investigating the phylogenetic history of toxin tolerance in mushroom-feedingEcology and evolution · 2023Article
- On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity.Immunogenetics · 2022Review
- Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system.Immunogenetics · 2021Article
- Markers for genetic change.Heliyon · 2021Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAdvances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.
resultsWe introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.
conclusionsTOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference. Software, a detailed manual, and example data files are available through github carolinafishes.github.io.
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