treemix 1.13

CQLS Software Support

2022-09-01 418 words 2 minutes

Contents

Installed

This software should be available with no extra configuration.

treemix-1.13

Link to Manual

TreeMix

Authors: JK Pickrell and JK Pritchard

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.

The details of the TreeMix model are presented in: Pickrell JK and Pritchard JK, Inference of population splits and mixtures from genome-wide allele frequency data.

Some extensions are presented in: Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, Güldemann T, Kure B, Mpoloka SW, Nakagawa H, Naumann C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante CD, Berger B, Tishkoff SA, Henn BM, Stoneking M, Reich D, Pakendorf B. The genetic prehistory of southern Africa.

We describe an application of this model to looking for natural selection in humans and dogs at Genomes Unzipped.

What’s new:

11/22/16

TreeMix 1.13 released in the download section.

Merges a bugfix branch from Mikkel Schubert that fixes a compilation error many users were coming across. Many thanks to Mikkel for the fix!

Location and version

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$ which treemix
/local/cluster/bin/treemix
$ treemix --version
TreeMix v. 1.13
$Revision: 231 $

help message

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$ treemix --help
TreeMix v. 1.13
$Revision: 231 $

Options:
-h display this help
-i [file name] input file
-o [stem] output stem (will be [stem].treeout.gz, [stem].cov.gz, [stem].modelcov.gz)
-k [int] number of SNPs per block for estimation of covariance matrix (1)
-global Do a round of global rearrangements after adding all populations
-tf [file name] Read the tree topology from a file, rather than estimating it
-m [int] number of migration edges to add (0)
-root [string] comma-delimited list of populations to set on one side of the root (for migration)
-g [vertices file name] [edges file name] read the graph from a previous TreeMix run
-se Calculate standard errors of migration weights (computationally expensive)
-micro microsatellite data
-bootstrap Perform a single bootstrap replicate
-cor_mig [file] list of known migration events to include (also use -climb)
-noss Turn off sample size correction
-seed [int] Set the seed for random number generation
-n_warn [int] Display first N warnings

software ref: https://bitbucket.org/nygcresearch/treemix/wiki/Home
research ref: https://doi.org/10.1371/journal.pgen.1002967