Science Score: 44.0%
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Low similarity (5.8%) to scientific vocabulary
Repository
Scripts for demographic modelling in moments
Basic Info
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Metadata Files
README.md
Demographic modelling
This repository includes scripts of demographic models to perform demographic analyses in moments.
12 models: 4 basic models adapted from Momigliano et al. (2020), IM (isolation with migration), AM (ancient migration), SC (secondary contact) and SI (strict isolation), as well as their variations with exponential (G) and instantaneous (Ne) effective population size changes.
The models assume data is provided in form of folded jAFS, in this case computed from a VCF using easySFS (https://github.com/isaacovercast/easySFS).
The Optimizations.py script is used for running multiple optimizations, adapted by Momigliano et al. (2020) from a pipeline by Daniel Portik (https://github.com/dportik).
100+ Database
Collection of 108 IM, AM, SC, SI, and two epoch scenarios with all combinations including ae (ancestral expansion), b (bottleneck), NeC (instantaneous effective population size changes), 2N (heterogenous selection), 2M (heterogeneous migration rates).
3-population scenarios:
Out of Africa model from Gutenkunst et al. (2009);
Two-splits model: Model with split between pop 1 and (2,3), then split between 2 and 3. Assumes 2 occurs in between populations 1 and 3, which do not come in to contact with one another. Migration is symmetrical between 'adjacent' population pairs (ie 1<->2, 2<->3, but not 1<->3);
One-split model: Model with simultaneous split between pop 1, 2 and 3. Migration is symmetrical between all population pairs (ie 1<->2, 2<->3, and 1<->3).
Citations:
Paolo Momigliano, Ann-Britt Florin, Juha Meril, Biases in Demographic Modeling Affect Our Understanding of Recent Divergence, Molecular Biology and Evolution, Volume 38, Issue 7, July 2021, Pages 29672985.
Owner
- Login: carolindahms
- Kind: user
- Repositories: 1
- Profile: https://github.com/carolindahms
Citation (CITATION.cff)
cff-version: 1.2.0
title: Demographic modelling in moments
message: "If you use this dataset, please cite it using the metadata from this file."
type: dataset
authors:
- given-names: "Carolin"
family-names: "Dahms"
orcid: 'https://orcid.org/0000-0002-3283-7820'
email: "carolin.dahms.ac@gmail.com"
date-released: "2021-07-18"
identifiers:
- type: url
value: "https://github.com/carolindahms/moments"
abstract: "Scripts of demographic models to perform demographic analyses in moments."
commit: e476f1329f979cb55e6437d73840c3ab289329e1
keywords:
- Demographic modelling
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