Installation

Download

The source code is avaible as a tarball and be download here [1]

Earlier versions from here: http://popgen.dk/software/download/angsd/

Install

Unpack the tarball

Unix

The software can be compiled using make

cd angsd0.43
make

zlib needs to be installed on your system.

Misc folder

Misc folder contains:

1. simnextgen a program for simulating genotype likelihoods
2. getUnfolded, simnextgen only outputs the true folded frequency spectra. getUnfolded uses the "true" genotypes to estimate the unfolded spectra.
3. testfolded/optimSFS uses the .sfs output from -realSFS 1 to estimate the site frequency spectra polarized to the ancestral type.