TreesimJ specifications


Unique identifier OMICS_11875
Name TreesimJ
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Output data Output options include writing traces, histograms and summary statistics from the data collectors in addition to sampled genetic sequences and genealogies.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Brendan O'Fallon <>

Publication for TreesimJ

TreesimJ in publication

PMCID: 4871536
PMID: 27191167
DOI: 10.1371/journal.pcbi.1004940

[…] chains were consistent when different tree priors (constant population size or bayesian skyline) were used ()., we first simulated the evolution of a gene with a constant evolutionary rate using treesimj []. the simulation was initiated from a randomly generated ancestor sequence with 450 nucleotides. the mutation rate was set to 0.0001 substitutions per site per generation and jukes-cantor […]

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TreesimJ institution(s)
Department of Genome Sciences, Seattle, WA, USA
TreesimJ funding source(s)
National Science Foundation Postdoctoral Research Fellowship (0906018); National Institutes of Health (5T32GM007464)

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