Limits...
forqs: forward-in-time simulation of recombination, quantitative traits and selection.

Kessner D, Novembre J - Bioinformatics (2013)

Bottom Line: forqs is a forward-in-time simulation of recombination, quantitative traits and selection.It was designed to investigate haplotype patterns resulting from scenarios where substantial evolutionary change has taken place in a small number of generations due to recombination and/or selection on polygenic quantitative traits. forqs is implemented as a command-line C++ program.Source code and binary executables for Linux, OSX and Windows are freely available under a permissive BSD license: https://bitbucket.org/dkessner/forqs.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095 and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

ABSTRACT

Summary: forqs is a forward-in-time simulation of recombination, quantitative traits and selection. It was designed to investigate haplotype patterns resulting from scenarios where substantial evolutionary change has taken place in a small number of generations due to recombination and/or selection on polygenic quantitative traits.

Availability and implementation: forqs is implemented as a command-line C++ program. Source code and binary executables for Linux, OSX and Windows are freely available under a permissive BSD license: https://bitbucket.org/dkessner/forqs.

Show MeSH

Related in: MedlinePlus

forqs chromosome representation. An individual chromosome is represented by a list of haplotype chunks. Each haplotype chunk is represented by two numbers (position, id): the position where it begins and the identifier of the founding haplotype from which it is derived. This cartoon depicts a chromosome with three haplotype chunks as the result of recombination (double crossover) between two founder chromosomes
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3928523&req=5

btt712-F1: forqs chromosome representation. An individual chromosome is represented by a list of haplotype chunks. Each haplotype chunk is represented by two numbers (position, id): the position where it begins and the identifier of the founding haplotype from which it is derived. This cartoon depicts a chromosome with three haplotype chunks as the result of recombination (double crossover) between two founder chromosomes

Mentions: forqs begins with a set of founding haplotypes carried by the individuals in the initial generation. Individuals are diploid and carry a user-specified number of chromosome pairs. By assigning a unique identifier to each founding haplotype, individual haplotype chunks are tracked as they recombine over subsequent generations (Fig. 1). For the purposes of simulation, any existing neutral variation on the haplotype chunks can be ignored, and only those loci with fitness effects need to be tracked.Fig. 1.


forqs: forward-in-time simulation of recombination, quantitative traits and selection.

Kessner D, Novembre J - Bioinformatics (2013)

forqs chromosome representation. An individual chromosome is represented by a list of haplotype chunks. Each haplotype chunk is represented by two numbers (position, id): the position where it begins and the identifier of the founding haplotype from which it is derived. This cartoon depicts a chromosome with three haplotype chunks as the result of recombination (double crossover) between two founder chromosomes
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928523&req=5

btt712-F1: forqs chromosome representation. An individual chromosome is represented by a list of haplotype chunks. Each haplotype chunk is represented by two numbers (position, id): the position where it begins and the identifier of the founding haplotype from which it is derived. This cartoon depicts a chromosome with three haplotype chunks as the result of recombination (double crossover) between two founder chromosomes
Mentions: forqs begins with a set of founding haplotypes carried by the individuals in the initial generation. Individuals are diploid and carry a user-specified number of chromosome pairs. By assigning a unique identifier to each founding haplotype, individual haplotype chunks are tracked as they recombine over subsequent generations (Fig. 1). For the purposes of simulation, any existing neutral variation on the haplotype chunks can be ignored, and only those loci with fitness effects need to be tracked.Fig. 1.

Bottom Line: forqs is a forward-in-time simulation of recombination, quantitative traits and selection.It was designed to investigate haplotype patterns resulting from scenarios where substantial evolutionary change has taken place in a small number of generations due to recombination and/or selection on polygenic quantitative traits. forqs is implemented as a command-line C++ program.Source code and binary executables for Linux, OSX and Windows are freely available under a permissive BSD license: https://bitbucket.org/dkessner/forqs.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095 and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

ABSTRACT

Summary: forqs is a forward-in-time simulation of recombination, quantitative traits and selection. It was designed to investigate haplotype patterns resulting from scenarios where substantial evolutionary change has taken place in a small number of generations due to recombination and/or selection on polygenic quantitative traits.

Availability and implementation: forqs is implemented as a command-line C++ program. Source code and binary executables for Linux, OSX and Windows are freely available under a permissive BSD license: https://bitbucket.org/dkessner/forqs.

Show MeSH
Related in: MedlinePlus