SEEDY specifications

Information


Unique identifier OMICS_26838
Name SEEDY
Alternative name Simulation of Evolutionary and Epidemiological DYnamics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.3
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/seedy_1.3.tar.gz
Maintained Yes

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Documentation


Publication for Simulation of Evolutionary and Epidemiological DYnamics

SEEDY citations

 (2)
library_books

Bayesian reconstruction of transmission within outbreaks using genomic variants

2018
PLoS Comput Biol
PMCID: 5927459
PMID: 29668677
DOI: 10.1371/journal.pcbi.1006117

[…] sample sequencing, and we used different methods to reconstruct the transmission history from sequencing and epidemiological data. To simulate pathogen evolution, first we simulated an outbreak using SEEDY [] (we used a fixed population of 15 hosts, one initial case, and a basic reproduction number of 1.43, see ); then, we translated the transmission history into a population history, and simulate […]

library_books

Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep Sequence Data

2017
Am J Epidemiol
PMCID: 5860558
PMID: 29149252
DOI: 10.1093/aje/kwx182

[…] us disease outbreaks with within-host pathogen evolution under various mutation rates and bottleneck sizes by simulation, using the R (R Foundation for Statistical Computing, Vienna, Austria) package Seedy (). In contrast to other simulation approaches, this method explicitly simulates within-host evolution and allows sampling of mixed pathogen populations across time. We expanded upon methods pre […]

SEEDY institution(s)
Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA

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