Genomes usually must be decoded several times over to get a complete and accurate sequence, but the first three billion bases of Neanderthal should “hit all the essential differences,” Dr. Egholm said.

The researchers’ hope is to recover the entire sequence of the Neanderthal genome, but that will depend on whether they can recover enough DNA. From sampling so far, no particular gaps in the sequence are apparent. “We are hitting all the chromosomes and getting good coverage,” Dr. Egholm said. If no single specimen yields a full sequence, the genome might be recovered by combining DNA from several individuals.

One of the most important results that researchers are hoping for is to discover, from a three-way comparison of chimp, human and Neanderthal DNA, which genes have made humans human. The chimp and human genomes differ at just 1 percent of the sites on their DNA. At this 1 percent, Neanderthals resemble humans at 96 percent of the sites, to judge from the preliminary work, and chimps at 4 percent. Analysis of these DNA sites, at which humans differ from the two other species, will help understand the evolution of specifically human traits “and perhaps even aspects of cognitive function,” Dr. Paabo said.

The degree of resemblance between humans and Neanderthals is fiercely debated by archaeologists, and even issues like whether Neanderthals had language have not been resolved. Dr. Paabo believes that genetic analysis is the best hope of doing so. He has paid particular attention to a gene known as FOXP2, which from its mutated forms in people seems to be involved in several advanced aspects of language.

A longstanding dispute among archaeologists is whether the modern humans who first entered Europe 45,000 years ago, ultimately from Africa, interbred with the Neanderthals or forced them into extinction. Interbreeding could have been genetically advantageous to the incoming humans, says Bruce Lahn, a geneticist at the University of Chicago, because the Neanderthals were well adapted to the cold European climate  the last ice age had another 35,000 years to run  and to local diseases.

Evidence from the human genome suggests some interbreeding with an archaic species, Dr. Lahn said, which could have been Neanderthals or other early humans.

So far no specific evidence of human-Neanderthal interbreeding has been found, Dr. Egholm said. But it may require analysis of almost the full Neanderthal genome to rule out all possibility of genetic interchange.