https://github.com/pdimens/2022-tatlanticus_popgen
Repository associated with the publication: Weak range-wide population structure in the blackfin tuna (Thunnus atlanticus) revealed by analysis of genome-wide SNPs
https://github.com/pdimens/2022-tatlanticus_popgen
population-genetics
Last synced: 9 months ago
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Repository associated with the publication: Weak range-wide population structure in the blackfin tuna (Thunnus atlanticus) revealed by analysis of genome-wide SNPs
- Host: GitHub
- URL: https://github.com/pdimens/2022-tatlanticus_popgen
- Owner: pdimens
- Created: 2021-01-05T15:23:43.000Z (almost 5 years ago)
- Default Branch: manuscript
- Last Pushed: 2023-03-01T19:36:46.000Z (over 2 years ago)
- Last Synced: 2024-12-08T22:17:44.895Z (10 months ago)
- Topics: population-genetics
- Language: Jupyter Notebook
- Homepage: https://doi.org/10.1093/icesjms/fsad012
- Size: 117 MB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Tatlanticus_popgen
Repository associated with the publication: Weak range-wide population structure in the blackfin tuna (Thunnus atlanticus) revealed by analysis of genome-wide SNPs found [here](https://doi.org/10.1093/icesjms/fsad012)
## What's included
- `amova`: Analysis of molecular variance
- `dapc`: Discriminant Analysis of Principal Components
- `faststructure`: fastSTRUCTURE analysis
- `fineradstructure`: fineRADstructure analysis
- `fst`: Pairwise (Hudson 1992) FST
- `inputfiles`: All the input files necessary to run any of the notebooks/analyses
- `isolationbydistance`: Constructing the least-cost paths for isolation-by-distance tests
- `kinship`: Kinship analysis with KING-robust and PCRelate
- `outlieranalysis`: Detecting putative outlier loci with BayPass, Bayescan, and outFLANK
- `pca`: Principal Component Analysis, Principal Coordinate Analysis, and Spatial Principal Component Analysis