THE MAXIMUM CONTRIBUTION FROM A SAMPLED ANCESTOR POPULATION TO A MORE RECENT POPULATION.
This software is a complement to the paper Sjödin et al 2014. There are four parts of the package corresponding to whether the maximum ‘genetic’ or maximum ‘demographic’ contribution is of interest and whether this is done using analytical formulas or simulations. The data should be in the form of a biallelic marker for which two samples from two populations separated by time have been obtained. A prerequisite is that there is some information regarding the number of generations that separates the two samples as well as some idea of a smallest (effective) population size of the population that supposedly evolved from the sampled older population to the more recent population. The programs in MaxCon can then be used to assess a maximum demographic/genetic contribution from the older population to the more recent that is consistent with the observed samples. There is a brief ‘Readme.txt’ included in the zipped file that should be consulted before running. The simulation code only requires R while the programs relying on the analytical formulas (written in Python and C++) depend on the MPFR and GMP libraries . Included is also some R code for plotting the results.
To use the (Linux) version, unzip and untar the files in an appropriate directory using
“tar xvzf MaxCon_v1.0.tar.gz”
and follow the instructions in Readme.txt.
Software history:
February 2014, release of version 1
If you experience any problems (the software has only been tested in an Ubuntu/Linux environment) , please email Per Sjödin.