Here, we upload all necessary files for the example of an application of **LDJump**.

- SimulatedPopulations.zip: This file contains three different simulation setups of 16 individuals (=sequences) with background rates of 0.001, 0.0054, and 0.001. This setup contains 15
*Hotspots*of 8 to 40 folds of the background rates evenly distributed across the sequence. - Lookups.zip: This file contains the lookup table of 100 sequences with a theta of 0.01 and the lookup table of 16 sequences with a theta of 0.01.

The required R-command for the estimation of the recombination map with **LDJump** for the recombination map with a background rate of 0.054 is the following:

```
require(LDJump)
results = LDJump("/pathToSample/HatLandscapeN16Len1000000Nrhs15_th0.01_540_1.fa", alpha = 0.05, segLength = 1000,
pathLDhat = "/pathToLDhat", format = "fasta", refName = NULL, thth = 0.01)
postscript("Results.eps", horiz = F)
plot(results[[1]], xlab = "Segments", ylab = "Estimated Recombination Rate", main = "Estimated recombination map with LDJump")
dev.off()
```

With the *plot*-Function of the package *stepR* one will obtain the estimated map with the estimated recombination rates plotted on the y-axis and the according segment number on the x-axis. The *postscript* and *dev.off* commands before and after plotting the results, respectively, will save the result in EPS-format.

**LDJump** returns a list of 7 elements which contains the estimated recombination map, the constant recombination rate estimates per segment, the calculated summary statistics (in a matrix), the type I error probability, the sample size, the sequence length and the segment lenght used.
For a constant recombination rate estimation only the latter six elements are returned.

Notes:
* Both ZIP-Files have to be unzipped before usage in the R-function *LDJump*.
* Runtime of one of these examples will be at least one hour.
* We recommend when *LDJump* is applied with different populations/examples simultaneously to create directories and start *LDJump* separately from these directories.

PhHermann/LDJump documentation built on July 5, 2018, 12:24 a.m.

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