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AdmixTools specifications

Information


Unique identifier OMICS_30041
Name AdmixTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C
Computer skills Advanced
Version 4.1
Stability Stable
Maintained Yes

Subtools


  • convertf
  • qp3Pop
  • qpBound
  • qpDstat
  • qpF4Ratio
  • rolloff

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Nick Patterson

Publication for AdmixTools

AdmixTools citations

 (148)
call_split

Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater

2018
Nat Commun
PMCID: 5893588
PMID: 29636446
DOI: 10.1038/s41467-018-03722-x
call_split See protocol

[…] s homologous to cow X chromosomal regions were excluded and the remaining SNPs were used for PSMC analyses and estimation of the relative cross coalescence rates. The f3-statistics was implemented in ADMIXtools. Bayes factor delimitation was employed in SNAPP and BEAST by estimating the marginal likelihood for each competing species delimitation model, and then Bayes factors, was used to assess s […]

library_books

The seasonal occupancy and diel behaviour of Antarctic sperm whales revealed by acoustic monitoring

2018
Sci Rep
PMCID: 5882826
PMID: 29615756
DOI: 10.1038/s41598-018-23752-1

[…] r provided a gain of 20 dB, and input was AC coupled with a nominal corner frequency (−3 dB point) of 6.6 Hz. A 6th order lowpass Butterworth filter with a corner frequency (−3 dB point) of 4 kHz and rolloff of 120 dB/decade served as the anti-aliasing filter. The analog-digital converter, based on an AD7683B chip, provided 100 dB of spurious free dynamic range, and a total signal-to-noise and dis […]

library_books

Hybridization and gene flow in the mega pest lineage of moth, Helicoverpa

2018
Proc Natl Acad Sci U S A
PMCID: 5948968
PMID: 29610329
DOI: 10.1073/pnas.1718831115

[…] To evaluate the possibility of admixture across the Helicoverpa phylogeny, we calculated the f3 statistic for all possible three-species combinations using AdmixTools v. 3.0 (). Only trios where f3 is negative are indicative of admixture between two source populations against a resulting target population. To populate a tree-like scenario for the estimat […]

library_books

Convergent genomic signatures of domestication in sheep and goats

2018
Nat Commun
PMCID: 5840369
PMID: 29511174
DOI: 10.1038/s41467-018-03206-y

[…] e the statistical relevance of possible admixture vectors identified by TreeMix (Supplementary Table ), we calculated the three-population test f3 as a formal test of genetic introgression, using the qp3Pop program of the ADMIXTOOLS suite for each combination of groups. For Capra, the wpCH group was divided between Australian breeds, French breeds, and Italian breeds. Results are reported in Suppl […]

library_books

Noise Source and Individual Physiology Mediate Effectiveness of Bird Songs Adjusted to Anthropogenic Noise

2018
Sci Rep
PMCID: 5834586
PMID: 29500452
DOI: 10.1038/s41598-018-22253-5

[…] of their category based on 5% and 95% frequency, 90% frequency bandwidth, peak frequency, aggregate entropy and average power,. Background noise was filtered below 1,500 Hz and above 12,000 Hz with a rolloff of 12 dB in Audacity and all were played at a standardised amplitude. We did not remove background noise from the adjusted songs frequencies themselves, because (1) we did not want to risk rem […]

library_books

New thin film surface electrode array enables brain mapping with high spatial acuity in rodents

2018
Sci Rep
PMCID: 5830616
PMID: 29491453
DOI: 10.1038/s41598-018-22051-z

[…] nsult, Frankfurt, Germany). The signals were acquired and amplified through a multichannel recording system (Lynx-8 amplifier system, amplification 8000 or 5000 times, butterworth filter: 1 Hz–9 kHz, rolloff: 12 dB per octave, Neuralynx, Bozeman, USA) and stored through AudiologyLab at a sampling rate of 25 kHz using a 32-channel MIO card (NI-6259 National Instruments, Austin, USA). The three deep […]

Citations

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AdmixTools institution(s)
Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Affymetrix, Inc., Santa Clara, CA, USA
AdmixTools funding source(s)
Supported by U.S. National Science Foundation HOMINID grant 1032255, and by National Institutes of Health grant GM100233.

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