msHOT 20080815 – modifying ms that allows Hotspots of Recombination and Gene Conversion

msHOT 20080815

:: DESCRIPTION

msHOT, modifying Hudson’s ms simulator, allows for implementation of multiple crossover hotspots and/or multiple gene conversion hotspots in the simulated genetic region.

::DEVELOPER

Garrett Hellenthal and Matthew Stephens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

msHOT

:: MORE INFORMATION

Citation:

Hellenthal, G and M. Stephens.
msHOT: modifying Hudson’s ms simulator to incorporate crossover and gene conversion hotspots.
Bioinformatics. 2007 Feb 15;23(4):520-1.

GenCo 200806 – Estimate Gene Conversion and Crossover Rates

GenCo 200806

:: DESCRIPTION

GenCo is program to estimate gene conversion and crossover rates in population genetic data

::DEVELOPER

McVean Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

GenCo

:: MORE INFORMATION

Citation

Gay J, Myers S, and McVean G (2007).
Estimating meiotic gene conversion rates from population genetic data.
Genetics 177:881-94.

HapBound-GC and SHRUB-GC – Detect Crossover and Gene-Conversion Recombinations

HapBound-GC and SHRUB-GC

:: DESCRIPTION

HapBound-GC and SHRUB-GC respectively compute lower and upper bounds on the minimum combined number of crossover and gene-conversion recombinations. SHRUB-GC constructs a graphical representation of evolutionary history involving coalescent, mutation, crossover and gene-conversion events.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows with Cygwin /MacOsX

:: DOWNLOAD

HapBound-GC and SHRUB-GC

:: MORE INFORMATION

Citation

Song, Y.S., Ding, Z., Gusfield, D., Langley, C.H., and Wu, Y.
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences
Lecture Notes in Computer Science 3909, (2006) 231-245.”

BARCE 1.2 – Bayesian Application for Recombination and Gene Conversion Estimation

BARCE 1.2

:: DESCRIPTION

BARCE (Bayesian Application for Recombination and Gene Conversion Estimation) is a C++ program for detecting recombination breakpoints in four-sequence alignments using hidden Markov models, Bayesian principles and Markov chain Monte Carlo sampling.

::DEVELOPER

Grainne McGuire and Dirk Husmeier

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
C++ compiler

:: DOWNLOAD

BARCE

:: MORE INFORMATION

Citation

Husmeier D., McGuire G. (2003):
Detecting Recombination in 4-Taxa DNA Sequence Alignments with Bayesian Hidden Markov Models and Markov Chain Monte Carlo,
Molecular Biology and Evolution 20(3):315-337.