The package ProteinEvolverABC is a computer framework to estimate recombination and substitution rates in multiple alignments of protein sequences by approximate Bayesian computation.
The package CodABC is computer framework to coestimate Recombination, Substitution and Molecular Adaptation (dN/dS) rates by approximate Bayesian computation from coding sequence alignments.
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.
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.
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.
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 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.
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.