RASPberry 202002 – Recombination via Ancestry Switch Probability

RASPberry 202002

:: DESCRIPTION

RASPberry is a software for recombination rate inference using ancestry switch points in admixed individuals.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

RASPberry

:: MORE INFORMATION

Citation

Nat Genet. 2011 Jul 20;43(9):847-53. doi: 10.1038/ng.894.
Recombination rates in admixed individuals identified by ancestry-based inference.
Wegmann D1, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Mosley T, Becker LC, Ruczinski I, Beaty TH, Kardia SL, Meyers DA, Barnes KC, Becker DM, Freimer NB, Novembre J.

HybridCheck v1.0.1 – Hybridisation Recombination and Introgression Detection and Dating

HybridCheck v1.0.1

:: DESCRIPTION

HybridCheck is a software package to visualise the recombination signal in large DNA sequence dataset, and it can be used to analyse recombination, genetic introgression, hybridisation and horizontal gene transfer.

::DEVELOPER

HybridCheck team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

HybridCheck

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2015 Sep 23. doi: 10.1111/1755-0998.12469. [Epub ahead of print]
HybridCheck: software for the rapid detection, visualisation and dating of recombinant regions in genome sequence data.
Ward BJ, van Oosterhout C.

rbrothers – Multiple Change-point Recombination Detection

rbrothers

:: DESCRIPTION

R package rbrothers provides easy access to recombination detection software DualBrothers and provides new functionality for pre-processing sequence data and post-processing DualBrothers output.

::DEVELOPER

rbrothers team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

rbrothers

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Jun 12;9:235-8. doi: 10.4137/EBO.S11945. Print 2013.
rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.
Irvahn J1, Chattopadhyay S, Sokurenko EV, Minin VN.

Heu-MCHC 1.0.2 – Heuristic Algorithm for the Haplotype Inference problem on Pedigree data with recombinations and mutations

Heu-MCHC 1.0.2

:: DESCRIPTION

Heu-MCHC is a fast and accurate heuristic for the Minimum-Change Haplotype Configuration (MCHC) problem, i.e. a combinatorial formulation of the haplotype inference problem on pedigree data where the total number of recombinations and point mutations has to be minimized.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

Heu-MCHC

:: MORE INFORMATION

Citation

Yuri Pirola, Paola Bonizzoni, and Tao Jiang.
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume: 9 , Issue: 1 Page(s): 12 – 25 (2011).

RDP 5.05 – Recombination Detection Program

RDP 5.05

:: DESCRIPTION

RDP (Recombination detection program) is software that applies a number of recombination detection and analysis algorithms. Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Complementary to a high degree of analysis flow automation, RDP also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. RDP can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000×10 kilobase sequences to 20×2 megabase sequences within 48 h on a desktop PC.

::DEVELOPER

Phylogenomics Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

RDP

:: MORE INFORMATION

Citation

Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. (2010).
RDP3: a flexible and fast computer program for analyzing recombination.
Bioinformatics 26, 2462-2463

SlidingBayes 0.94 – Exploring Recombination using a Sliding window approach based on Bayesian Phylogenetic inference

SlidingBayes 0.94

:: DESCRIPTION

SlidingBayes is a tool for Bayesian scanning analysis to detect recombination or discordant phylogenetic relationships throughout a nucleotide or amino acid alignment. Bayesian scanning resembles the bootscanning analysis in the way that Bayesian inference analysis is performed in a sliding window of a specified length, and the support of every single clade (approximate posterior probabilities instead of the bootstrap values) is plotted throughout the alignment.

::DEVELOPER

Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research

:: SCREENSHOTS

:: REQUIREMENTS

Linux / WIndows / MacOsX
Java

:: DOWNLOAD

SlidingBayes

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Apr 1;21(7):1274-5. Epub 2004 Nov 16.
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.
Paraskevis D1, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM.

Recomb – Simulate Genetic Datasets with Recombination Rates Changing Over Time

Recomb

:: DESCRIPTION

The program ms_recomb, a modified version of Richard Hudson’s ms, uses the coalescent to simulate genetic datasets with recombination rates that change through time.

The program msstats_recomb, an extensively modified version of Kevin Thornton’s msstats, implements n-tuple subsampling and calculates a suite of summary statistics with specific focus on recombination events

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

Recomb

:: MORE INFORMATION

Citation:

Cox, M.P., B.R. Holland, M.C. Wilkins and J. Schmid. 2013.
Reconstructing Past Changes in Locus-Specific Recombination Rates.
BMC Genet. 2013 Feb 25;14:11. doi: 10.1186/1471-2156-14-11.

IMgc – Generates Recombination-free Sequences from Recombination-rich Multiple Sequence Alignments

IMgc

:: DESCRIPTION

IMgc reads recombination-rich multiple sequence alignments, and returns the largest block containing no four-gamete violations.

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ windows/MacOsX
Perl

:: DOWNLOAD

IMgc

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 15;23(14):1851-3.
Recombination-filtered genomic datasets by information maximization.
Woerner AE, Cox MP, Hammer MF.

HotspotFisher – Detect Recombination Hotspots from Population Polymorphism data

HotspotFisher

:: DESCRIPTION

HotspotFisher is a package for detecting recombination hotspots from population polymorphism data. HotspotFisher uses a multi-hotspot model and the truncated weighted pairwise log-likelihood (TWPLL), so it can detect multiple hotspots in a region. HotspotFisher can be used to both phased/haplotype and unphased/genotype data directly, with arbitrary levels of missing data.

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows

:: DOWNLOAD

HotspotFisher

:: MORE INFORMATION

Citation

Jun Li, Michael Q Zhang, Xuegong Zhang (2006)
A New Method for Detecting Human Recombination Hotspots and Its Applications to the HapMap ENCODE Data.
The American Journal of Human Genetics 79:628-639.

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

DTU Health Tech

:: 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