Felix Chandrakumar’s separate Neanderthal, Denisovan and Clovis Anzick tools have been retired in favor of a combined calculator that will compare your DNA to 31 archaic and ancient samples. It is 131 MB and can be freely downloaded here:
Felix explains, “The tool checks for small segments chunks within the DNA to see how much they are identical. You need to remove the genealogical perspective and put on the general idea that every human is 99.7% identical. This tool tells you how much of that 0.3 is identical. Instead of SNP by SNP, which mostly match each other by 60 to 70%, it checks smaller chunks of identical segments.
The 99.7% is based on each SNP comparison. If we do the same, everyone will match at ~60%. The only problem is, that does not tell the true shared DNA but shared SNPs. If we compare smaller segments as in genetic genealogy like 1 cM some will never match and that’s not true either. However, the goal here is to find shared DNA which is a thin blurred line between both. So, the idea here is to take identical chunks of small segments greater than 100k positions also considering for runs of Homozygosity, the percentage of matching is calculated. The reason why 100k is considered is because most gene lengths fall within this length range and the noise/accidentaloccurrence range of 1-2% is acceptable.”
I ran the raw data of a few family members through the archaic tools and came up with these results:
More can be found out about each individual ancient sample and its age here. All of the samples in the tool are uploaded to Gedmatch and are available to run your kit against with the one to one utility.
Ongoing discussion of the Ancient and Archaic tools at FTDNA forums can be found here.