https://github.com/smithsonian/fabaceae_phylogenomics_workflow
Target-enrichment data processing in legumes
https://github.com/smithsonian/fabaceae_phylogenomics_workflow
legumes molecular-evolution phylogenetics target-enrichment
Last synced: 6 months ago
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Target-enrichment data processing in legumes
- Host: GitHub
- URL: https://github.com/smithsonian/fabaceae_phylogenomics_workflow
- Owner: Smithsonian
- Created: 2017-08-15T15:44:42.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2023-06-11T13:31:31.000Z (about 3 years ago)
- Last Synced: 2025-07-21T15:44:43.694Z (about 1 year ago)
- Topics: legumes, molecular-evolution, phylogenetics, target-enrichment
- Homepage:
- Size: 783 KB
- Stars: 6
- Watchers: 7
- Forks: 2
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Fabaceae phylogenomics workflow
This repository contains instructions on handling target-enrichment (bait-capture) data using [HybPiper](https://github.com/mossmatters/HybPiper) and performing subsequent phylogenetic analyses on the Smithsonian Institution HPC (Hydra cluster). If you don't have your own dataset, you can use tutorial data from [here](https://github.com/mossmatters/HybPiper/tree/master/test_dataset). If you don't have access to the cluster, install all [dependencies](https://github.com/mossmatters/HybPiper#dependencies) and programs used here such as MAFFT, TrimAl, RAxML on your system and run the main commands from the job files. Follow steps in the [Data_processing.md](https://github.com/Smithsonian/Fabaceae_Phylogenomics_workflow/blob/master/Data_processing.md).
Paper:
Vatanparast, M., A. Powell, J. J. Doyle, and A. N. Egan. 2018. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. [Applications in Plant Sciences 6(3): e01036](https://onlinelibrary.wiley.com/doi/full/10.1002/aps3.1036)
Datasets are available from Figshare: https://doi.org/10.6084/m9.figshare.c.4040372.v4
Example phylogenetic trees using different species tree reconstruction methods.
