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ARGweaver specifications


Unique identifier OMICS_32376
Name ARGweaver
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
License MIT License
Computer skills Advanced
Stability Stable
nose, pyflakes, pep8
Maintained Yes




No version available


  • person_outline Adam Siepel

Publication for ARGweaver

ARGweaver citations


A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

R Soc Open Sci
PMCID: 5367300
PMID: 28386436
DOI: 10.1098/rsos.160805

[…] To determine when and on which specific allele selection occurred, we used the coalescent framework implemented in ARGWeaver []. ARGWeaver models the coalescent process across non-recombining blocks of sequences and thus provides access to the evolutionary history of DNA sequences. It allows recovering several sta […]


Inferring Past Effective Population Size from Distributions of Coalescent Times

PMCID: 5105851
PMID: 27638421
DOI: 10.1534/genetics.115.185058

[…] equences, to be able to compare these population size profiles to previously published results. Hence, we have to find a way to obtain the gene genealogies from sequence data. One way could be to use ARGWeaver (), as is done in . However, found a systematic bias in their reconstruction of effective population size over time profiles when using ARGWeaver to infer gene genealogies, even for rather […]


Inference of Ancestral Recombination Graphs through Topological Data Analysis

PLoS Comput Biol
PMCID: 4988722
PMID: 27532298
DOI: 10.1371/journal.pcbi.1005071
call_split See protocol

[…] We performed 4,000 simulations of a sample of 40 sequences with 12 segregating sites, using the software ARGweaver []. The population was simulated using a coalescent infinite sites model with recombination. The population-scaled recombination rate, ρ, was randomly generated in each simulation, taking va […]


Genes with monoallelic expression contribute disproportionately to genetic diversity in humans

Nat Genet
PMCID: 4942303
PMID: 26808112
DOI: 10.1038/ng.3493

[…] expression status and its TMRCA in presence of confounding variables. For each gene, mean TMRCA over the entire transcribed region was calculated from genome-wide TMRCA estimates generated by running ARGWeaver on Complete Genomics data. The log-transformed TMRCA was regressed under the following model: log(TMRCA)=β0+β1IMAE∕BAE+β2length+β3r+β4exprlevel+β5exprbreadth+β6Z where IMAE/BAE is an indicat […]


ARG walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis

BMC Genomics
PMCID: 4682399
PMID: 26679564
DOI: 10.1186/1471-2164-16-S12-S1

[…] construction algorithm [] followed by integrating these recombination events into a subARG; ACG [] estimates the full likelihood of the ARG using a Bayesian Markov chain Monte Carlo (MCMC) procedure; ARGweaver [] can infer ARGs from genome-wide data based on hidden Markov models (HMM).In this paper, we propose a graph mining method, namely ARG-walker, to infer the different strengths of a recombin […]


Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies

PMCID: 4566269
PMID: 26224734
DOI: 10.1534/genetics.115.177980

[…] from five Yorubans from Ibadan, Nigeria (YRI) and five Utah residents of central European descent (CEU) from the 1000 Genomes pilot project () and previously analyzed for the same purpose (). We used ARGweaver () to obtain a sample path of local genealogies for the two populations (YRI and CEU). The parameters used were 200 change points, a mutation rate of μ=1.26×10−8, and a recombination rate of […]


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ARGweaver institution(s)
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
ARGweaver funding source(s)
Supported by a David and Lucile Packard Fellowship for Science and Engineering, NIH/NIGMS grant GM102192 and postdoctoral fellowships from the Cornell Center for Comparative and Population Genomics.

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