Tag: Recombination

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.

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.

SNPsim 0.8 – Coalescent Simulation of Hotspot Recombination

SNPsim 0.8

:: DESCRIPTION

SNPsim is a population genetic simulator that generates samples of SNP (Single Nucleotide Polymorphisms) haplotypes and diploid biallelic genotypes.

::DEVELOPER

Phylogenomics Group @ the University of Vigo, Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 SNPsim

:: MORE INFORMATION

Citation

Posada D and Wiuf C. 2003.
Simulating haplotype blocks in the human genome.
Bioinformatics 19: 289-290.

msHOT 20080815 – modifying ms that allows Hotspots of Recombination and Gene Conversion

msHOT 20080815

:: DESCRIPTION

msHOT, modifying Hudson’s ms simulator, allows for implementation of multiple crossover hotspots and/or multiple gene conversion hotspots in the simulated genetic region.

::DEVELOPER

Garrett Hellenthal and Matthew Stephens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 msHOT

:: MORE INFORMATION

Citation:

Hellenthal, G and M. Stephens.
msHOT: modifying Hudson’s ms simulator to incorporate crossover and gene conversion hotspots.
Bioinformatics. 2007 Feb 15;23(4):520-1.

3SEQ 1.1.0812 – Software for Detecting Recombination in Sequence data

3SEQ 1.1.0812

:: DESCRIPTION

3SEQ is a software program for identifying mosaic structure or recombination in nucleotide sequence data. 3SEQ takes as input a data set with a minimum of three aligned sequences, and it tests whether any sequence in the data set is a recombinant or mosaic of any other two sequences in the data set.

::DEVELOPER

the Mathematical Modeling and Bioinformatics Group at the Oxford University Clinical Research Unit (OUCRU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • C++ Compiler

:: DOWNLOAD

  3SEQ 

:: MORE INFORMATION

Citation

Boni MF, Posada D, Feldman MW.
An exact nonparametric method for inferring mosaic structure in sequence triplets.
Genetics, 176:1035-1047, 2007.

DualBrothers 1.1 – Recombination Detection Software

DualBrothers 1.1

:: DESCRIPTION

DualBrothers is a recombination detection software based on the dual Multiple Change-Point (MCP) model. This model allows for changes in topology and evolutionary rates across sites in a multiple sequence alignment.

::DEVELOPER

Marc A. Suchard, M.D., Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Java virtual machine

:: DOWNLOAD

 DualBrothers

:: MORE INFORMATION

Citation

Minin VN, Dorman KS, Suchard MA.
Dual multiple change-point model leads to more accurate recombination detection,
Bioinformatics, 21:3034-3042, 2005.

biomc2 1.9 – Detect recombination in DNA Sequence Alignments

biomc2 1.9

:: DESCRIPTION

 biomc2 is a hierarchical Bayesian procedure to detect recombination in DNA sequence alignments based on the incongruence between topologies caused by recombinational events.

::DEVELOPER

Leonardo de Oliveira Martins

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 biomc2

:: MORE INFORMATION

Citation

Leonardo de Oliveira Martins, élcio Leal and Hirohisa Kishino (2008)
Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees.
PLoS ONE 3(7): e2651.

DRIVeR – Diversity Resulting from In Vitro Recombination

DRIVeR

:: DESCRIPTION

The program DRIVeR is applicable to libraries generated by recombining two highly homologous parent sequences differing at only a few (e.g. ≤20) nucleotide or amino acid positions.

DRIVeR Online Version

::DEVELOPER

Andrew Firth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C++ Compiler
:: DOWNLOAD

 DRIVeR

:: MORE INFORMATION

Citation

AndrewE. Firth, Wayne M. Patrick, 2005,
Statistics of protein library construction,
Bioinformatics, 21, 3314-3315.

IRiS – Identification of Recombinations in Sequences

IRiS

:: DESCRIPTION

IRiS produces a subARG in two phases by given a collection of haplotypes. A combinatorial algorithm called the DSR is a model-based approach to detecting recombinations in haplotypes (with a guaranteed approximation factor). The algorithm is based on iteratively classifying sets of lineages as dominant, subdominant or recombinant (DSR). In the first phase, DSR is run multiple times with different sets of parameters and statistical consensus is derived from them to produce a matrix of recombination information called the recomatrix. This encodes the local topology information of only the high confidence recombination events detected in the first phase. The subARG is constructed from the recomatrix in the second phase

::DEVELOPER

IBM Computational Biology Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 IRiS

:: MORE INFORMATION

Citation

Javed, A., Pybus, M., Melé, M., Utro, F., Bertranpetit, J., Calafell, F., and Parida, L.,
IRiS: Construction of ARG network at genomic scales,
Bioinformatics (2011) 27 (17): 2448-2450.