ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.


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THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions

Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files.

The main documentation for this is found here:


  1. Generate .saf files from each population using ANGSD SFS Estimation
    1. using a 2D-SFS as a prior, estimated using ngs2dSFS
    2. using marginal spectra as priors, estimated using realSFS


More information here:


If you use these methods, you should cite the m. fumagalli paper