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 hundreds of unphased sequences.
You can download a java program package implemented the method from this website. The current version (v0.2) including source codes can be downloaded here. A readme file is here. A data set simulated assuming a two-epoch model can be downloaded here. If you have questions about the usage of the package, please contact the author (Xiaoming Liu). Note: The current version does not support missing data.
UPDATE (May 29, 2015): Some users with Java 1.6 on their system cannot run java classes with simpleGUI.jar, which is compiled with Java 1.7. For those users please download this simpleGUI.jar and replace the original one coming with the package. As some users asked for help regarding the usage of the package, I compiled a FAQ and will keep updating it.
UPDATE (June 5, 2015): Some users may have trouble running the program Stairway_plot_output_summary because of the GUI. Here I provide a commandline version of the program. It asks for the folder containing all the .addTheta files, mutation rate, generation time and output file name. Just type "java Stairway_plot_output_summary_commandline" to see a brief usage guidance.
UPDATE (October 9, 2015): Some users asked for a commandline version of of the Stairway_plot_input_bootstrap. You can download it from here. It asks for the original input file and the number of bootstrap sample. Just type "java Stairway_plot_input_bootstrap_commandline" to see a brief usage guidance.
UPDATE (June 10, 2016): Stairway plot v2 is now released for beta test. The new version can be applied to both unfolded SFS and folded SFS and uses subsampling to control overfitting. It can be downloaded here. A readme file is here.
April 6, 2014: Stairway plot package version 0.1 is released.
April 29, 2014: A data set simulated assuming a two-epoch model is available for testing purposes.
November 3, 2014: Stairway plot package version 0.2 is released.
May 29, 2015: simpleGUI.jar compiled with java 1.6 is provided. A FAQ is provided.
June 5, 2015: a commandline version of Stairway_plot_output_summary is provided.
June 10, 2016: Stairway plot package v2 beta is released.
Cite the work:
Liu X and Fu YX. (2015) Exploring population size changes using SNP frequency spectra. Nature Genetics. 47(5):555-559.