single locus msBayes (download)
Uses hierarchical approximate Bayesian computation (HABC) for comparative (multi-taxa) phylogeographic inference. HABC allows testing hypotheses and estimating hyper-parameters that quantify levels and patterns of congruence across co-distributed taxon-pairs in divergence/colonization times and/or categorical biogeographic histories (i.e. recent colonization/expansion vs range stability).
Contributors = Wen Huang, Yan Qi, Naoki Takebayashi, Eli Stahl and Mike Hickerson
Multi taxa/ Multi Locus msBayes - MTML-MSBAYES (with rate heterogeneity across loci)
Available Here
MTML-MSBAYES Manual
MTML-MSBAYES Installation
R scripts for use with generic or msBayes ABC (Contributors = Wen Huang and Mike Hickerson)
Generic simulation testing of ABC conditions using PODS (pseudo-observed data sets)
simulation testing of MTML-MSBAYES conditions using PODS (pseudo-observed data sets)
Shell script (run on command line)
R script (runs within the above shell script)
Categorical model choice with ABC (e.g. testing for migration vs isolation across taxon-pairs or estimating any other discrete integer parameter)
Plotting N-dimensional euclidian distances between observed summary statistic vector and accepted simulated summary statistic vectors
ABC Testing Kit (download)
These scripts can be used to test different ABC algorithms. Specifically, one can compare the sufficiency of different sets of summary statistics for particular parameters. Secondarily, one can use them to determine estimator accuracy and bias under different simulation models and ABC algorithms (i.e. tolerance, transformation procedure, and number of prior simulations).
Contributors = Wen Huang and Mike Hickerson