TOAST

TOAST is an R software package designed to help researchers analyze transcriptomic data by identifying orthologous sequences. It uses the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to perform ortholog searches and generate multiple sequence alignments. TOAST automates the process of generating locus and concatenated alignments, and allows users to explore missing data patterns and reassemble alignments based on their needs. The software is open source and can be easily integrated into existing or novel custom informatic pipelines for phylogenomic inference.

Topic

Phylogenomics;Transcriptomics;Plant biology;Proteomics;RNA-Seq

Detail

  • Operation: Transcriptome assembly;Sequence alignment;Visualisation;Deposition;Genotyping

  • Software interface: -

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: -

  • Version name: -

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Alex Dornburg dornburgalex@gmail.com ,Simon Gilroy sgilroy@wisc.edu

  • Collection: -

  • Maturity: -

Publications

  • Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly.
  • Wcisel DJ, et al. Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. 2020; 20:41. doi: 10.1186/s12862-020-01603-w
  • https://doi.org/10.1186/S12862-020-01603-W
  • PMID: 32228442
  • PMC: PMC7106827

Download and documentation

< Back to DB search