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


No version available



  • person_outline Brendan O'Fallon

Publication for TreesimJ

TreesimJ citations


Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV 1 Infection

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

[…] 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 s […]


Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations

PMCID: 4844292
PMID: 27137364
DOI: 10.3390/plants2010016

[…] oalescent simulations, sampled alleles are traced back via the simulation of gametogenesis until the most recent-common-ancestor (MRCA) has been found []. A tree-based forward-time simulation system, TreeSimJ [], has also been developed, however. Programs such as ms [] and simCoal [] are coalescent simulation programs able to simulate genealogies and infer demography and population structure among […]

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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