Sueoka and Lobry declared respectively that, in the absence of bias between the 
two DNA strands for mutation and selection, the base composition within each 
strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). 
However, the genome sequences of many bacteria, vertebrates and viruses showed 
asymmetries in base composition and gene direction. To determine the 
relationship of base composition skews with replication orientation, gene 
function, codon usage biases and phylogenetic evolution, in this paper a program 
called DNAskew was developed for the statistical analysis of strand asymmetry 
and codon composition bias in the DNA sequence. In addition, the program can 
also be used to predict the replication boundaries of genome sequences. The 
method builds on the fact that there are compositional asymmetries between the 
leading and the lagging strand for replication. DNAskew was written in Perl 
script language and implemented on the LINUX operating system. It works quickly 
with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta 
format. The source code is freely available for academic use at 
http://www.epizooty.com/pub/stat/DNAskew.