PSPE - Phylogenetic Simulation of Promoter Evolution
Version 0.86, Copyright(c) 2006 Weichun Huang

--ABOUT-- 

PSPE is designed to run simulation of sequence evolution of related species, especially, for evolution simulation of promoter sequences containing functional cis-regulatory elements.  Different from other evolution simulation programs, PSPE simulates sequence evolution under the neutral evolution model and uses function constraints as natural selection forces in species evolution.

--INSTALLATION--
This is a Linux binary distribution containing executable files for both 32 (pspe_Linux_x86_32) and 64 bits (pspe_Linux_x86_64) systems. The pspe_Linux_x86_64 only runs on 64 bits Linux System. 

a) Uncompress the distribution by running the following command:

   tar xfj PSPE-Linux.tar.bz2

b) Copy the correponding executalbe file to one of system default executable file directories such as ${HOME}/bin or /usr/local/bin
   for example for 32 bits system:

    cp PSPE-Linux-Bin/pspe_Linux_x86_32 $HOME/bin/pspe
    
    OR
   
    cp PSPE-Linux-Bin/pspe_Linux_x86_32 $HOME/bin/pspe

--USAGE--
	pspe -[VHSM]  paraFile
       -V: show version information
       -H: show help information
       -S: do not output sequences
       -M: do not output motif information

--PARAMETER CONFIGURE FILE--

All PSPE simulation parameters (e.g Phylogenetic Tree, functional constraints and motifs) are specified in one simulation configure file. Each parameter consists of a Name and a Value in the form of 'NAME=VALUE", where values can be a single numeric/character value or a vector of many numeric and character values.  A character value should be enclosed in double quotation, and a vector should be enclosed by brackets, in which individual values are separated by a comma.

Parameter Examples: 
  Length=5000
  MatrixDir="./matDir"
  PWM={"E2F", "FOS"}
  BaseFreqs={0.258, 0.242, 0.242, 0.258}
  Model  = "HKY"
  Params = {0.05}

For a complete example, see file paraExample.psp in example sub-directory.
