rush 1.4 – Recombination detection Using SHustrings

rush 1.4

:: DESCRIPTION

rush is a fast computer program for testing the null hypothesis of no recombination using for pairs of unaligned DNA sequences.

::DEVELOPER

Bernhard Haubold 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 rush

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 15;29(24):3121-7. doi: 10.1093/bioinformatics/btt550. Epub 2013 Sep 23.
An alignment-free test for recombination.
Haubold B1, Krause L, Horn T, Pfaffelhuber P.

VDJSeq-Solver – in Silico VDJ Recombination Detection tool

VDJSeq-Solver

:: DESCRIPTION

VDJSeq-Solver is a completely automated workflow for the in silico detection of the main clone V(D)J recombination sequence characterizing neoplastic tissues, using RNA-Seq paired-end reads.

::DEVELOPER

EDA (Electronic Design Automation Group)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • TopHat
  • Java
  • Perl
  • BEDTools
  • Bowtie
  • Blast
  • SHRiMP
  • Samtools

:: DOWNLOAD

 VDJSeq-Solver

:: MORE INFORMATION

Citation

VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool.
Paciello G, Acquaviva A, Pighi C, Ferrarini A, Macii E, Zamo’ A, Ficarra E.
PLoS One. 2015 Mar 23;10(3):e0118192. doi: 10.1371/journal.pone.0118192.

Recodon 1.6.0 / NetRecodon 6.0 – Coalescent Simulation of Intracodon Recombination

Recodon 1.6.0 / NetRecodon 6.0

:: DESCRIPTION

Recodon is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general time-reversible model of nucleotide substitution with a proportion of invariable sites and among-site rate variation. In addition, the program implements non-reversible processes and mixtures of different codon models.

NetRecodon  is a population genetic simulator that generates samples of nucleotide and codon sequences from haploid/diploid populations with intracodon recombination, migration, growth and dated tips. It can also run in several processors using MPI.

::DEVELOPER

the Posada lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 RecodonNetRecodon

:: MORE INFORMATION

Citation:

Arenas, M. and Posada, D. 2007.
Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography.
BMC Bioinformatics, 8:458.

Arenas M. and Posada, D. 2010.
Coalescent simulation of intracodon recombination.
Genetics, 184(2): 429-437.

CodABC 2.0.0 – Coestimation of Recombination, Substitution and Molecular Adaptation Rates by Approximate Bayesian Computation

CodABC 2.0.0

:: DESCRIPTION

The package CodABC is computer framework to coestimate Recombination, Substitution and Molecular Adaptation (dN/dS) rates by approximate Bayesian computation from coding sequence alignments.

::DEVELOPER

Dr. MIGUEL ARENAS

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  CodABC

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.
CodABC: A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation.
Arenas M, Lopes JS, Beaumont MA, Posada D

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

SlidingBayes

:: 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.