File	Date	Author	Commit
SimBac	2011-10-01	Weigang Qiu	[2327fd] initial depository
codon-usage-table.txt	2011-10-01	Weigang Qiu	[2327fd] initial depository
make-coalescence-tree.pl	2011-10-01	Weigang Qiu	[2327fd] initial depository
readme.txt	2011-10-01	Weigang Qiu	[1b6a26] modify readme file
sample-output-gen-1000.fas	2011-10-01	Weigang Qiu	[2327fd] initial depository
sim-single-pop.config	2011-10-01	Weigang Qiu	[2327fd] initial depository
sim-single-pop.pl	2011-11-09	Weigang Qiu	[afdf22] fix POD documentation

Read Me

The SimBac package simulates bacterial genome evolution.

Included files:

sim-single-pop.pl:
	Simulating evolution of a single population

sim-mixed-pop.pl:
	Simulating two populations, allowed to mix & recombine

sim-isolated-pop.pl:
	Simulating two isolated populations, NOT allowed to mix & recombine

make-coalescence-tree.pl:
	Post-simulation processing

SimBac/CodonType.pm:
	Required module

SimBac/CodonFreqTable.pm:
	Required module

SimBac/RandCDS.pm:
	Required module

SimBac/Convert.pm:
	Required module

codon-usage-table.txt:
	Sample codon usage table

sim-single-pop.config:
	Sample settings for simulating genome evolution in a single popualtion

sim-mixed-pops.config:
	Sample settings for simulating divergence of two mixed popualtions

sim-isolated-pops.config:
	Sample settings for simulating divergence of two isolated popualtions

sample-output-gen-1000.pl:
	Sample alignment output

External Dependencies:
	 Moose
	 BioPerl
	 Math::Random::MT::Auto
	 Algorithm::Numerical::Sample
	 Statistics::Basic