Dataset Open Access

How much does Ne vary among species? Site Frequency Spectrum data

Galtier, Nicolas; Rousselle, Marjolaine


This directory contains Site Frequency Spectra (SFS) data analyzed by Galtier & Rousselle 2020, https://www.biorxiv.org/content/10.1101/861849v1

All files are in DoFE format (see http://www.lifesci.susx.ac.uk/home/Adam_Eyre-Walker/Website/Software.html), with the additional #unfolded annotation when required.

There are four subdirectories:

- primates_fruitflies: unfolded SFS from 5 species of primates and 5 species of fruitflies, all mutations and GC-conservative mutations only.
- Rousselle_et_al_2019: unfolded SFS from 50 species from 10 groups of animals, all mutations and GC-conservative mutations only.
- Chen_et_al_2017: folded SFS from 23 species of animals, all mutations; please note that the Chen et al. 2017 SFS, although folded, are encoded as unfolded for consistency.
- Galtier_2016: unfolded SFS from 28 species of animals, all mutations.

Example command lines:

#Gamma
multi_grapes1.1 -in primates_fruitflies.dofe -out pf.csv -model GammaZero -fold
#Gamma+lethal, plth=0.6
multi_grapes1.1 -in primates_fruitflies.dofe -out pf.csv -model GammaZero -p_lethal 0.6 -fold
#Reflected Gamma+lethal, plth=0.6
multi_grapes1.1 -in primates_fruitflies.dofe -out pf.csv -model ReflectedGamma -p_lethal 0.6 -fold
#Gamma+lethal, plth=0.6, unfolded
multi_grapes1.1 -in primates_fruitflies.dofe -out pf.csv -model GammaZero -p_lethal 0.6

 

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