Mars, the maker of Snickers, M&M’S, Milky Way and other confections, announced two years ago that it would spend $10 million over five years to sequence and analyze the cocoa genome, in a project involving the Department of Agriculture, I.B.M. and some academic collaborators. The analysis is only now getting under way in earnest.

Dr. Shapiro said a goal of the project was to make sure the genetic data was available for all to use without intellectual property restrictions. Those gaining access to the data on the group’s Web site www.cacaogenomedb.org have to agree not to patent anything, like specific genes, from their findings.

He said that while Mars would gain from larger supplies and potentially lower prices for cocoa, the company would have no special advantage over other companies.

“We have a sustainable supply of cocoa, but so does everybody else,” he said.

Mark J. Guiltinan, a professor of plant molecular biology at Penn State, a leader of the other effort, said his group also intended to make its data freely available, though it would not explicitly prohibit others from patenting inventions made by using the research.

Dr. Guiltinan said the new genetic information could lead to chocolate that tastes better and contains more flavonoids, ingredients that scientists think may be healthful. He said one of his graduate students spent five years isolating and studying just four genes involved in making flavonoids.

“After we sequenced the genome,” he said, “we got all the genes in a couple of days.”

Dr. Guiltinan said there had initially been efforts to do one genome project, but that Mars and the Agriculture Department “decided to go it alone, so we decided to keep doing what we had planned to do.”