Evidence map›Paper›PMID 37398279›Full record

ArticlebioRxiv : the preprint server for biology2023

dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra.

Xin Huang, Travis J Struck, Sean W Davey, Ryan N Gutenkunst

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Xin Huang
Travis J Struck
Sean W Davey
Ryan N GutenkunstORCID 0000-0002-8659-0579

Funding

Joint inferences of natural selection between sites and populationsR01GM127348 · NIGMS · UNIVERSITY OF ARIZONA · PI GUTENKUNST, RYAN · 2019 to 2023
$1.7M
Population genomic inferences of history and selection across populations and timeR35GM149235 · NIGMS · UNIVERSITY OF ARIZONA · PI Ryan Gutenkunst · 2023 to 2026
$1.3M
NIGMS NIH HHS R01 GM127348NIGMS NIH HHS R35 GM149235
6 · The paper itself

Abstract

Summary: dadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing. Availability and Implementation: dadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available at https://github.com/xin-huang/dadi-cli . dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2 https://cacao.jetstream-cloud.org/ .

Identifiers

PMID37398279
PMCPMC10312675

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.