Method for estimating admixture parameters of constant migration using admixture fractions and all data for the corresponding paper.
For performance reasons, we use cython to speed up calculations. For this, you need a working toolchain for building C code (gcc and clang are known to work). Since you are going to build Python extensions, you will need python development headers (e.g. on ubuntu linux the package name is python-dev). Also our method uses numpy and scipy packages.
To build the package use
$ cd lamom
$ python setup.py build_ext -i
To run this method k-statistics k1, k2 and k3 of admixture proportions for each chromosome of population that admixed only in founding generation are required. To estimate parameters simply run
python run.py --file data.txt
You may test this script using dummy_data.txt file, that included in the repository. True parameters for this file are Te=0 and Td=10.
-N specifies an effective population size.
-Te0 and -Td0 sets initial point for the optimisation algorithm.