SEEDY specifications


Unique identifier OMICS_26838
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
Maintained Yes




No version available


Publication for Simulation of Evolutionary and Epidemiological DYnamics

SEEDY citations


Bayesian reconstruction of transmission within outbreaks using genomic variants

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 […]


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

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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