ADMIXTOOLS (or AdmixTools) is an
R software package that is primarily used for analyzing admixture in
population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and pop ...
. The initial version was originally developed by
Nick Patterson and colleagues in 2012.
The second reimplemented version, ADMIXTOOLS 2, which has a revised
point-and-click
Point and click are the actions of a computer user moving a pointer to a certain location on a screen (''pointing'') and then pressing a button on a mouse, usually the left button (''click''), or other pointing device. An example of point and cli ...
interface and improved speed, was developed jointly by Nick Patterson and
David Reich.
qpGraph
qpGraph is a software program that is part of the ADMIXTOOLS software package developed by
Patterson Patterson may refer to:
People
* Patterson (surname)
Places
;Canada
* Pattersons Corners, Ontario
*Patterson Township, Ontario
*Patterson, Calgary a neighbourhood in Calgary, Alberta.
;United States of America
* Patterson, Arkansas
*Patterson, C ...
et al. (2012). qpGraph builds graphs that model
genetic admixture
Genetic admixture occurs when previously diverged or isolated genetic lineages mix.⅝ Admixture results in the introduction of new genetic lineages into a population.
Examples
Climatic cycles facilitate genetic admixture in cold periods and gene ...
in population relationships.
It estimates network topology
likelihoods from a fixed number of admixture events, based on the observed
f-statistics
In population genetics, ''F''-statistics (also known as fixation indices) describe the statistically expected level of heterozygosity in a population; more specifically the expected degree of (usually) a reduction in heterozygosity when compared ...
.
Other tools
Related statistical tools in the ADMIXTOOLS software package include qpAdm, qpDstat, and qpWave.
qpDstat and qpWave test to see if populations form
clade
A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...
s, while qpAdm estimates ancestry proportions.
See also
*
SplitsTree
SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. SplitsTree impleme ...
*
Dendroscope
Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures. Dendroscope can be used for a variety of analyse ...
*
List of phylogenetics software
This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenie ...
References
External links
ADMIXTOOLS 2– inferring demographic history from genetic data
AdmixToolsat
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous ...
qpGraph software packagein Bioconductor 3.8.
admixr– R package for reproducible analyses using ADMIXTOOLS
Phylogenetics software
Free R (programming language) software
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