MIMAR 20101217 – MCMC Estimation of the Isolation-Migration model Allowing for Recombination

MIMAR 20101217

:: DESCRIPTION

MIMAR (MCMC estimation of the Isolation-Migration model Allowing for Recombination) is a Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. It uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and in contrast to previous methods, allows for intralocus recombination. Note that you need to know the ancestral allele at each polymorphic site in order to calculate the summary statistics.

::DEVELOPER

Céline Becquet

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MIMAR

:: MORE INFORMATION

Citation:

Becquet and Przewroski (2007)
A new approach to estimate parameters of speciation models with application to apes
Genome Res. 2007. 17: 000

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

:: 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.

VDJsolver 1.0b – Analysis of Human Immunoglobulin VDJ Recombination

VDJsolver 1.0b

:: DESCRIPTION

VDJsolver is a program that analyses human immunoglobulin VDJ recombination. The indetification of V and J genes is performed using standard sequencial alignment against databases of functional VH and JH genes from the IMGT database

::DEVELOPER

CBS (Center for Biological Sequence Analysis),  Technical University of Denmark

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

VDJsolver

:: MORE INFORMATION

Citation

No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements.
Ohm-Laursen L, Nielsen M, Larsen SR, and Barington T.
Immunology. 119(2):265-77. 2006