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xiaoming-liu / stairway-plot-v2

The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data.
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Stairway Plot v2

About

The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data. It does not need a pre-defined population model and can be applied to thousands of unphased sequences.

Major changes to v1

Significant improvement in terms of 1) the application to both folded and unfolded SFSs, 2) overfitting control, 3) speed, 4) support for masking out part of the SFSs and 5) usage convenience.

The executable package of stairway plot v2 can be downloaded here. A detailed readme file for running the programs can be found here.

Please cite 1 & 2

  1. Liu X and Fu YX. (2015) Exploring population size changes using SNP frequency spectra. Nature Genetics. 47(5):555-559.
  2. Liu X and Fu YX. (2020) Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Submitted.