Tag: Recombination

ProteinEvolverABC – Estimation of Recombination and Substitution Rates in Alignments of Protein Sequences

ProteinEvolverABC

:: DESCRIPTION

The package ProteinEvolverABC is a computer framework to estimate recombination and substitution rates in multiple alignments of protein sequences by approximate Bayesian computation.

::DEVELOPER

CME Group

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

ProteinEvolverABC

:: MORE INFORMATION

Citation

Arenas M.
ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation.
Bioinformatics. 2021 Aug 27:btab617. doi: 10.1093/bioinformatics/btab617. Epub ahead of print. PMID: 34450622.

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

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

Graham & McNeney Labs

:: 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.

RCandy 1.0.0 – Visualising Homologous Recombinations in Bacterial Genomes

RCandy 1.0.0

:: DESCRIPTION

RCandy is an R package for visualising homologous recombination events in bacterial genomes

::DEVELOPER

Chrispin Chaguza

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

RCandy

:: MORE INFORMATION

Citation:

Chaguza C, Tonkin-Hill G, Lo SW, Hadfield J, Croucher NJ, Harris SR, Bentley SD.
RCandy: an R package for visualising homologous recombinations in bacterial genomes.
Bioinformatics. 2021 Dec 2:btab814. doi: 10.1093/bioinformatics/btab814. Epub ahead of print. PMID: 34864895.

SWeBLAST – Look for Recombinations in non-aligned Sequences using BLAST

SWeBLAST

:: DESCRIPTION

SWeBLAST (Sliding Window Web-based BLAST) is a perl program that looks for recombinations in non-aligned sequences using BLAST.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 SWeBLAST

:: MORE INFORMATION

Citation

Fourment M, Gibbs AJ, Gibbs MJ.
SWeBLAST: a Sliding Window Web-based BLAST tool for recombinant analysis.
J Virol Methods. 2008, 152, 98-101

forqs 2015 – Forward-in-time Simulation of Recombination, Quantitative traits, and Selection

forqs 2015

:: DESCRIPTION

forqs is a forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. forqs also also models quantitative traits and selection on those traits.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 forqs

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 15;30(4):576-7. doi: 10.1093/bioinformatics/btt712. Epub 2013 Dec 10.
forqs: forward-in-time simulation of recombination, quantitative traits and selection.
Kessner D1, Novembre J.

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

Przeworski lab

:: 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

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

 Recodon , NetRecodon

:: 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.