Description of programs and tutorials
Here, you can find the programs we discussed, having a short summary about the programs and their inner working and a short tutorial of the program.
The program Structure (download website uses genotpyic data to assign individuals to populations probabilistically.
The program dadi (download website uses the site frequency spectrum to evaluate complex population models, up to three populations.
The program treemix download website
The program Geneland (it is an R package an can be installed from any CRAN site - see instructions)
The program Sate estimates a phylogenetic tree and aligns sequences at the same time.
RevBayes is a very versatile Bayesian inference system geared towards phylogenetic analysis. It has an R-like interface with its own language Rev.
BEAST 1.8 Skyline
Beast is a versatile package to analyze phylogenies population expansion and plots of parameters through time.
BEAST 2.3 SNAPP
SNAPP allows to estimate a species tree from unlinked single nucleotide polymorphims (SNP).
IMa estimates divergence times and population sizes and migration rates among populations using sequence data.
Migrate estimates population sizes, migration rates, and (in a very recent version) divergence times and among populations using sequence or microsatellite data.