Stairway plot v1.5
- an update to the original Stairway plot method
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 hundreds of unphased sequences.
Major changes
1. Stairway_plot_theta_estimation03 uses tuned parameters for the DE algorithm and the speed is improved. The default dimFactor is 2000.
2. Stairway_plot_output_summary02 summarizes the effective population size trajectory calculated for each bootstrap sample, and at each time point T, the median of a total of B estimates of the effective population size is used as the final estimate of Ne at T.
2. Stairway_plot_output_summary02 summarizes the effective population size trajectory calculated for each bootstrap sample, and at each time point T, the median of a total of B estimates of the effective population size is used as the final estimate of Ne at T.
Availability
Stairway plot v1.5 can be downloaded here.
Please cite 1 & 2:
- Liu X and Fu YX. (2015) Exploring population size changes using SNP frequency spectra. Nature Genetics. 47(5):555-559.
- Liu X. (2020) Human prehistoric demography revealed by the polymorphic pattern of CpG transitions. Molecular Biology and Evolution 37(9):2691-2698. [PDF]
Office3720 Spectrum Boulevard, Suite 304
Tampa, FL 33612 |
Telephone813-974-9865
|
xiaomingliu@usf.edu
|