•        0

Development of exact and approximate methods (Importance Sampling and MCMC based) for computing likelihoods under the standard population genetic models of mutation,migration amp; recombination. Project issues are mainatined at



Related Projects

Abnotc - rejectiono sampling for approximate bayesian computation

A suite of programs to do approximate bayesian computation. Does rejection sampling of coalescent simulations.

Gye-coalescence - Coalescence Simulation and Analysis Framework

A Java 5 based framework for coalescence based simulations and analysis of sample configurations. At the moment the main objective is to be able to simulate the evolution of microsatellite sequences (cSSRp's) and analyze generated sample configurations.

Finance-nscc-insurance - Interact with NSCC Insurance file transmissions

A framework to simplify reading, storing and coalescing data from NSCC Insurance standard files.

Snap-mcmc - SNP and AFLP data analysis: full coalescent analysis without those pesky gene trees.

Implementation of an MCMC based method for inferring species (population) trees and demographics from unlinked SNP data. Full description of method is in Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N., RoyChoudhury, A. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution (in press) This code is an add-on to beast2 More information at

Bio-dimsum - DIM SUM: Demography and Individual Migration Simulated Using a Markov chain

DIM SUM: Demography and Individual Migration Simulated Using a Markov chainDIM SUM (Demography and Individual Migration Simulated Using a Markov chain) is a stand-alone Java program for the simulation of population demography and individual migration, while keeping track of genetic relationships. It does not rely on assumptions of the coalescent or of discrete population boundaries. It is extremely flexible, allowing the user to set the positions of borders, the reaction of an organism to a bord

Jpropeller - A simple implementation of property objects (Props) as an easier alternative to standar

Jpropeller provides Prop objects that replace the normal JavaBean convention of methods like getName() and setName(). These first-class properties allow for many more features to be implemented easily: Notification of changes anywhere in the data model Calculated properties with efficient cached lazy evaluation Mirroring of data using paths within the data model Automatic UI generation More efficient UI updating via change coalescing Full Model-View system allowing for flexible reuse of UI compo

Treesimj - A flexible, forward-time population genetic simulator

TreesimJ is a forward-time simulator of an evolving population that tracks the evolutionary tree of the entire population. The application offers an intuitive GUI, a variety of pre-configured models of fitness, mutation, and demography, and a suite of data collectors that analyze the population and emit data to one or more sources. To the user, TreesimJ offers a simple, easy to use interface, a variety of interchangeable 'models' describing many aspects of the evolving population, and many ways

Pypopgen - A Population Genetics and Genomics library in Python

pyPopGen is a library to do Population Genetics (and Genomics) in Python. Although the library implements certain key concepts in population genetics (e.g. Fst statistics) it strives to use and facilitate the use of existing programs. It allows to use programs like Genepop, Arlequin, fdist2, Simcoal2, ... By usage we mean a mix of preparing input files, parsing output formats, using webservices, and offering new functionality on top of existing programs (e.g. easy creation of demographies for us

CVS Email Commit Notification

The enclosed Python scripts differ from most other commit notification solutions in that they coalesce all of the commit operations from a single \\\quot;cvs commit\\\quot; command into a single email. Most other solutions will send one email per directory.

Beast-mcmc - BEAST, a program for Bayesian MCMC of Evolution & Phylogenetics using Molecular Seq

BEAST, Bayesian Evolutionary Analysis Sampling Trees, is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is orientated towards (strict and relaxed) molecular clock analyses. It can be used as a method of constructing phylogenies, but it is also intended for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. It uses an XML