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Block-bootstrap procedure

FP Fanny Pouyet

Last updated date: Jul 21, 2020 Views: 1287 Forks: 0

original An abbreviated version of this protocol was published in eLife in Aug, 2018
Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences
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All the scripts used are available on Dryad. https://datadryad.org/stash/dataset/doi:10.5061/dryad.t76fk80


I used R to do the blockbootstrap strategy (there is a source code to estimate them):

confidence Intervals

The blockbootstrapped SFS to make demographic inferences are computeed using the functions matsplitter and booti from SFS_bootstrap.R
If you want to estimate confidence intervals of the SFS you wiil have to use the functions matsplitter as well as booti.2pop or booti.allpop


And the demographic inferences files are these ones : 

Supplementary file - settings files for demographic inferences

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Pouyet, F(2020). Block-bootstrap procedure. Bio-protocol Preprint. bio-protocol.org/prep409.
  2. Pouyet, F., Aeschbacher, S., Thiéry, A. and Excoffier, L.(2018). Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. eLife. DOI: 10.7554/eLife.36317

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