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.”

SelSim 2.1 – Simulate Population Genetic Data with Selection and Recombination

SelSim 2.1

:: DESCRIPTION

SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recombining region within which a single bi-allelic site has experienced natural selection. SelSim allows simulation from either a fully stochastic model of, or deterministic approximations to, natural selection within a coalescent framework. A number of different mutation models are available for simulating surrounding neutral variation. The package enables a detailed exploration of the effects of different models and strengths of selection on patterns of diversity.

::DEVELOPER

Chris C A Spencer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/WIndows

:: DOWNLOAD

SelSim

:: MORE INFORMATION

Citation

Spencer C., Coop, G. (2005)
SelSim: A program to simulate population genetic data with selection and recombination.
Bioinformatics. 2004 Dec 12;20(18):3673-5.

SIRENS – SImulating REcombination in Nucleotide Sequences

SIRENS

:: DESCRIPTION

SIRENS (SImulating REcombination in Nucleotide Sequences) is a free program written in MATLAB for simulating recombination in DNA sequence alignments of four sequences.

::DEVELOPER

Dirk Husmeier

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Matlab

:: DOWNLOAD

SIRENS

:: MORE INFORMATION

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.

Recco 0.93 – Recombination Analysis Using Cost Optimization

Recco 0.93

:: DESCRIPTION

Recco (Recombination Analysis Using Cost Optimization) analyzes alignments of sequences that evolved subject to recombination and mutation. The analysis provides evidence as to whether a dataset contains recombination, which sequence is a recombinant and where the recombination breakpoints are. The analysis is based on explaining one sequence with all other sequences in the alignment using mutation and recombination. A parametric analysis of the parameter alpha, which weights recombination cost against mutation cost, yields additional information as to which sequence might be recombinant.

::DEVELOPER

Jochen Maydt

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

Recco

:: MORE INFORMATION

Citation:

Maydt, J. and T. Lengauer (2006).
“Recco: Recombination Analysis Using Cost Optimization.”,
Bioinformatics 2006, 22(9):1064-1071, doi:10.1093/bioinformatics/btl057.