ExposedPrograms

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.

Genepop

Genepop on the Web and Genepop Software This software calculates standard population genetic quantities, such as FST, isolation by distance measures etc.

Theory; Tutorial material: download GENEPOP_TUTORIAL.ZIP

Structure

The program Structure (download website uses genotpyic data to assign individuals to populations probabilistically.

Theory Tutorial Example Report

Dadi

The program dadi (download website uses the site frequency spectrum to evaluate complex population models, up to three populations.

Theory Tutorial Example Report

Treemix

The program treemix download website

Theory Tutorial Example Report

Geneland

The program Geneland (it is an R package an can be installed from any CRAN site - see instructions)

Theory Tutorial Example Report

Sate

The program Sate estimates a phylogenetic tree and aligns sequences at the same time.

Theory Tutorial Example Report

RevBayes

RevBayes is a very versatile Bayesian inference system geared towards phylogenetic analysis. It has an R-like interface with its own language Rev.

Theory Tutorial Example Report

BEAST 1.8 Skyline

Beast is a versatile package to analyze phylogenies population expansion and plots of parameters through time.

Theory Tutorial Example Report

BEAST 2.3 SNAPP

SNAPP allows to estimate a species tree from unlinked single nucleotide polymorphims (SNP).

Theory Tutorial Example Report

IMa

IMa estimates divergence times and population sizes and migration rates among populations using sequence data.

Theory Tutorial Example Report

Migrate

Migrate estimates population sizes, migration rates, and (in a very recent version) divergence times and among populations using sequence or microsatellite data.

Theory Tutorial Example Report