The main thesis of the creationist paper falls apart once you understand the underhanded tricks that they use to get their 70%. To the uninitiated, it may seem like a subtle difference, but it isn't. The author uses a non-gapped alignment.
That was my first suspicion, the second would be ignoring reversed sequences that still accomplish the same functions.
The author of the creationist paper has rigged the methodology to ignore gaps, and therefore return a false result.
We have seen this type of intentionally misusing science in other areas, such as carbon 14 dating and living animals (seals at McMurdo Sound, etc), and several other dating methodologies.
First of all. There is no ONE result number. The algorithm compared about 650000 sequences with about 400 million bases in summary (Human Y is 60 million bases long, Chimp Y is about 20 million bases long). So compared sequences overlaped many times. I also got mismatch bases. Each sequence had (in my case) percentage identity, sequence length and number of mismatch bases. For example:
97.3% 4552 105
My guess is that the algorithm is similar to other matching algorithms (such as tree rings) ...
So they take one as the baseline and then compare the second one starting with matching both at one end and then shifting the second one along the first one base at a time, recording the degree of matching for each step.
The DNA likely has a lot of regions that were duplicated and then modified, so those would produce matches with lower percentages.
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