Citation¶

If Fstic contributes to work you publish, please cite the software release.

Software¶

Ruiz-Rodriguez, P. and Coscolla, M. Fstic: allele-frequency-based genetic distance calculator. Zenodo. doi:10.5281/zenodo.16813662

@software{fstic,
  author    = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
  title     = {Fstic: allele-frequency-based genetic distance calculator},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.16813662},
  url       = {https://github.com/PathoGenOmics-Lab/fstic}
}

The DOI above always resolves to the latest release. Zenodo also mints a version-specific DOI for each release, which is the better one to cite if the exact version matters for reproducibility.

The estimators¶

Fstic implements published estimators. Cite the original alongside the software for whichever you used.

`--formula`	Reference
`gst`, `fst`	Nei, M. (1973) Analysis of gene diversity in subdivided populations. PNAS 70(12):3321-3323.
`jost_d`	Jost, L. (2008) GST and its relatives do not measure differentiation. Molecular Ecology 17(18):4015-4026.
`reynolds`	Reynolds, J., Weir, B.S. and Cockerham, C.C. (1983) Estimation of the coancestry coefficient. Genetics 105(3):767-779.
`nei`	Nei, M. (1972) Genetic distance between populations. The American Naturalist 106(949):283-292.
`chord`	Cavalli-Sforza, L.L. and Edwards, A.W.F. (1967) Phylogenetic analysis: models and estimation procedures. Evolution 21(3):550-570.
`rogers`	Rogers, J.S. (1972) Measures of genetic similarity and genetic distance. Studies in Genetics VII, University of Texas Publication 7213:145-153.
`bray-curtis`	Bray, J.R. and Curtis, J.T. (1957) An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs 27(4):325-349.

Say which FST

--formula fst is the Nei (1973) formulation summed per locus, not the Weir & Cockerham (1984) theta estimator. Worth stating explicitly in a methods section, since readers assume the latter.

Authors¶

Paula Ruiz-Rodriguez and Mireia Coscolla, at I2SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia, Spain.

Part of PathoGenOmics Lab.