This repository contains all of the source code required to reproduce our paper on ancient directional migration using an extention of
pipelines/contains two different pipelines which implement all of the analyses in the paper. The first uses
msmc2to analyse real data from the SGDP and HGDP. The second uses
scrmto simulate demographic scenarios and does inference with
msmc. For instructions on reproducing these results, see directions in these directories. As a forewarning, these analyses are highly computationally intensive and may take several weeks or months of compute to run completely.
data/contains all of the relevant results from the
pipelines/directory used in the paper, and in the plots.
r/contains scripts for reproducing all of the plots from the paper. Note that
r/MASTER.r, if run by itself, contains all of the code necessary to create all the plots using the data in the
plot/has the output of the
r/directory, which are the plots used in the paper.
LaTeXsource for the actual manuscript of the paper.
analysescontains configuration files for the different analyses performed using the pipelines. Similarly,
lib/has some useful files for the plotting scripts.
To reproduce the analysis completely, please install the required
conda environment. This allows us to package a majority of the software dependencies together. There are several methods to install
conda, see here for details. Once
conda is installed, create the environment for this analysis from our list of dependencies:
conda env create -f envs/aaa.yml
This will create a
conda environemnt called
aaa. Activate it:
conda activate aaa
There are a couple of dependencies that are not included in
conda and must be installed manually.
msmc2must be installed from the Github source here.
admixrmust be installed from Github as well.