Software

 

popABC

#SUMMARY:

PopABC is an Approximate Bayesian Computation (ABC) method to estimate historical demographic parameters (e.g. population size, migration rate, mutation rate, recombination rate, splitting events) within a Isolation with migration (IM) population model.

popABC
This software is freeware and the source code is available.
It has been developed in the University of Reading by Mark Beaumont and Joao Lopes.
For any queries regarding the software join its google group.


#DOWNLOAD PACKAGES:

Win 98/Me/2000/XP (3,300Kb) download.
UNIX (2,609Kb) download.
MAC OSX (2,605Kb) download.
source code (2,457Kb) download.

User Guide (396Kb) download.
Lopes et al - 2009 (139Kb) download.
Lopes et al - 2009 Supplementary Information (98Kb) download.


#popABC LINKS:

Mailing list (http://groups.google.com/group/popabc)

Project home (http://code.google.com/p/popabc)


#FEATURES:

>Test population trees using standard "Isolation with Migration" model events:
 - population splitting events;
 - migration events.

>Can be used in two different formats:
 - with an user-friendly menu (command line-based);
 - strictly command line-based executables.

>Use recombination events

>use an unlimited number of populations

>Use two different DNA data types separately or at the same time:
 - Microssatelites DNA;
 - DNA Sequence.

>Use an unlimited number of loci from different DNA types:
 - nuclear DNA;
 - X-linked DNA;
 - Y-linked DNA;
 - mitochondrial DNA.

>Use different combinations of summary statistics:
 - Microssatelites DNA: 6;
 - DNA Sequence: 11.

>Estimate historical demographic parameters:
 - size of the populations;
 - splitting time between populations;
 - migration rates;

>Estimate genetic population parameters:
 - mutation rate (in one locus or among several loci);
 - recombination rate (in one locus or among several loci).

>Use two different mutation models:
 - Microssatelites DNA: stepwise mutation
 - DNA sequence: infinite-sites mutation

>Use several different prior distributions:
 - generalized gamma distribution;
 - uniform distribution;
 - normal and lognormal distributions;
 - beta distribution.

>Compare different models for the same analysis:
 - between different migration patterns;
 - with migration vs without migration;
 - with recombination vs without recombination;
 - between topologies of 3-population models;
 - between different branching histories (3 or more populations models);

#RELATED LINKS:

IM - A program for fitting the "Isolation with Migration" populational model using a Markov chain Monte Carlo method (Jody Hey, Rasmus Nielsen):
http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm