coalesceR: A pedagogical tool to teach the basics of coalescent theory

Coalescent theory provides a powerful modeling tool for population genetics. It is based on a genealogical interpretation of the history of gene lineages in populations. Although classical population genetics theory considers the evolution of gene lineages forward in time, coalescent theory considers the genealogical history of a sample of genes, looking backward in time. In the absence of selection (i.e., if all genetic variants are selectively neutral), then the mutation process can be decoupled from the genealogical process. Therefore, selectively neutral mutations can then be superimposed on the genealogical history. This package is intended to provide a pedagogical tool to teach the basics of coalescent theory. It enables to simulate gene genealogies in an isolated population of constant effective size, or in a population that changed in size some generations in the past. Gene genealogies can be constructed using a continuous time approximation, or a generation-by-generation algorithm.Graphical outputs show the consequence of population size changes on the shape of genealogies. Mutations can then be added on the gene genealogies, and summary statistics (e.g., heterozygosity, number of alleles) can be computed from gene histories.

Author
Renaud Vitalis <vitalis@supagro.inra.fr>.
Date of publication
2014-11-04 20:27:04
Maintainer
Renaud Vitalis <vitalis@supagro.inra.fr>
License
GPL (>= 2)
Version
0.2

View on R-Forge

Man pages

add.mutations
Add Mutations on a Coalescent Tree
coalesceR
A Pedagogical Tool to Teach the Basics of Coalescent Theory
coalesceR-internal
Internal coalesceR Function
draw.tree
Draw a Coalescent Tree
heterozygosity
Compute the Heterozygosity of a Sample of Genes
number.of.alleles
Compute the Number of Alleles in a Sample
sim.tree
Simulate a Coalescent Tree
TMRCA
Compute the TMRCA of a Coalescent Tree

Files in this package

coalesceR/DESCRIPTION
coalesceR/NAMESPACE
coalesceR/R
coalesceR/R/coalesceR.R
coalesceR/man
coalesceR/man/TMRCA.Rd
coalesceR/man/add.mutations.Rd
coalesceR/man/coalesceR-internal.Rd
coalesceR/man/coalesceR.Rd
coalesceR/man/draw.tree.Rd
coalesceR/man/heterozygosity.Rd
coalesceR/man/number.of.alleles.Rd
coalesceR/man/sim.tree.Rd
coalesceR/src
coalesceR/src/SimulateCoalescentTree.c