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

QuasiRecomb 1.2 – Inference of Quasispecies subjected to Recombination

QuasiRecomb 1.2

:: DESCRIPTION

QuasiRecomb is a software of Inference of Quasispecies subjected to Recombination.RNA viruses are present in a single host as a population of different but related strains. This population, shaped by the combination of genetic change and selection, is called quasispecies. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. We offer an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and tested by applying to reads obtained from experimental HIV samples.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 QuasiRecomb

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Feb;20(2):113-23. doi: 10.1089/cmb.2012.0232.
Probabilistic inference of viral quasispecies subject to recombination.
Töpfer A, Zagordi O, Prabhakaran S, Roth V, Halperin E, Beerenwinkel N.

stepwise 0.3 – Stepwise Detection of Recombination Breakpoints

stepwise 0.3

:: DESCRIPTION

A stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints.

::DEVELOPER

SFU Statistical Genetics working group

:: REQUIREMENTS

:: DOWNLOAD

 stepwise

:: MORE INFORMATION

Citation

Graham, McNeney and Seillier-Moiseiwitsch.
Stepwise detection of recombination breakpoints in sequence alignments.
Bioinformatics. 2005 Mar 1;21(5):589-95. Epub 2004 Sep 23.

iRSpot-Pse6NC 2.0 – Identifying Recombination Hotspots in Saccharomyces Cerevisiae

iRSpot-Pse6NC 2.0

:: DESCRIPTION

Based on dataset containing both ORF and non-ORF recombination sites, iRSpot-Pse6NC is a predictor which using SVM classifier by incorporating the key hexamer features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution feature selection approach.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae.
Yang H, Yang W, Dao FY, Lv H, Ding H, Chen W, Lin H.
Brief Bioinform. 2019 Oct 21. pii: bbz123. doi: 10.1093/bib/bbz123

iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC.
Int J Biol Sci. 2018 May 22;14(8):883-891. doi: 10.7150/ijbs.24616. eCollection 2018.
Yang H, Qiu WR, Liu G, Guo FB, Chen W, Chou KC, Lin H.

RDP 4.69 – Recombination Detection Program

RDP 4.69

:: 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

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

Jan Irvahn, Vladimir Minin

:: 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.

HybridCheck v1 – Hybridisation Recombination and Introgression Detection and Dating

HybridCheck v1

:: 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.

RASPberry 20141128 – Recombination via Ancestry Switch Probability

RASPberry 20141128

:: 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.

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

CodABC 2.0.0b

:: 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