About PSPE

PSPE is a computational tool specifically designed for simulating evolution of non-coding DNA sequences, in particular promoter sequences. PSPE, like other simulation tools, can use many different DNA substitution models and Insertion/Deletion models to simulate sequence evolution. What makes PSPE unique is that PSPE can perform sequence evolution under a set of user-specified functional constraints, e.g., GC contents, functional site locations, and distances between functional sites, which makes simulation more realistic. In addition, PSPE can, using a Poisson process for branching and a Exponential model for branch length, generate a random evolutionary tree of different topologies. The outputs of PSPE include simulated sequences, the alignment of sequences, and the location map of functional sites in each sequence. PSPE is a useful tool for studying evolution mechanisms and for evaluating alignment tools as well.

Availability and Citation

PSPE is freely available to public and can be downloaded at the following link.

PSPE for both 32 and 64 bits Linux systems (1MB)

Please use the following command to extract files from the compressed file: tar xvfj PSPE-Linu-Bin.tar.bz2, then follow the instructions in the README file for installation and usage.

PSPE should be cited as
Weichun Huang, Joseph R Nevins, and Uwe Ohler, Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessing their impact on alignment tools, Genome Biology, Vol 8 (10) 2007


TFBS PWM for evolution simulation (359B)

Supplementary Results

Additional results on MSA tool evaluation (437KB)

Note: some above files for download are in *.tar.gz format (use command 'tar xfz afile.tar.gz' to extract files). If you would like to have other data or programs used in our paper, please feel free to contact me.

R Graphics Output

TFBS Detection Accuracy of Turnover Sites in Aligning Five Mammal Species

TFBS Detection Accuracy (Average)
TFBS Detection Accuracy (YY1E2F)
TFBS Detection Accuracy (Pax6)
TFBS Detection Accuracy (IRF2)
TFBS Detection Accuracy (TP53)
TFBS Detection Accuracy (PPARG)
TFBS Detection Accuracy (ROAZ)


Clarice R. Weinberg, Ph.D.
Principal Investigator
Tel 984-287-3697
[email protected]