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I am doing simulations using a program 'ms':

https://snoweye.github.io/phyclust/document/msdoc.pdf

If you look at page 3 of this pdf, it explains the output produced by ms. The line which starts with positions tells us the position of segregating sites. But it is between 0 and 1. My simulation produces a chromosome of length 1.1Mb and I want to divide it into 100kb subwindows each. However, I don't know quite understand how I should determine which segregating site (which is a float number) falls into which sub window.

Can someone explain how this can be done?

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  • $\begingroup$ To simulate long sequences, it is preferred to use more recent simulators such as msprime or scrm. They are much faster and more user friendly. $\endgroup$ – user172818 Jun 3 at 15:59

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