about OMEGA

OMEGA was established at University of Rennes1, France, (Institute of Genetics and Development of Rennes, CNRS-umr6061), to automates the analysis of selective constraints acting on genes across evolution. It is readily useful as a web server for all researches that require codon-based (nucleotide) sequence alignmnent and nucleotide substitution rates calculation. OMEGA is available as a downloadable archive for independent installation.

OMEGA web server provides features like:

Builds multi-species gene sequence alignment.
Provides codon-based interspecies alignment using the corresponding protein alignment. The codon alignments are used to calculate the rate of nucleotide substitutions in coding sequence based on their impact on the encoded amino acid residue.
The server calculates dN and dS values using the codeml program of PAML.
Calculates the ratio of silent to replacement nucleotide substitution rates (ω = dN/dS) to provide an indicator to assess negative (ω << 1), neutral (ω = 1) or positive (ω > 1) selection acting on genes.
It can analyze pseudogenes as it takes into account the presence of in-frame mutation or stop-codon.
It is designed to analyse any number (<100) of orthologous genes, and thus is not limited to pairwise analysis.
The server also provides a batch mode analysis, with up to 100 sequences that can be submitted at the same time.
In batch mode, dN and dS values and ω ratio can be assessed by statistical tests to detect the presence or absence of selection in the query set versus pre-computed or personal benchmark set.

http://dogs.genouest.org/OMEGA