Not exactly, as your further comments make clear. SIFTER is not making trees based on evolutionary phylogeny. It is just inferring the trees directly from the data; the sequences include all the information needed to construct the tree and place the sequences into it.
Not it does not. It is critical to stay on topic here.
We are not testing for design. Instead, we are asking if similarity is fully explained by common function, or if is better explained by common descent.
If the answer is “common descent” that just could mean that God created by a process of common descent.
This is just totally false, both in the conclusion and the reasoning.
BLAST is a very complex algorithm, and much of that complexity enables it to run so fast. It takes a us a several weeks to cover all the key concepts for graduate students to understand how it works. It works fast because it relies on SEVERAL very clever heuristics.
So what? BLAST does not represent common design. We are not discussing design. It does, however, represent sequence similarity.
Here you are revealing some deep confusion.
SIFTER does not rely on information external to the sequences themselves when constructing the tree. What you are proposing is not even possible, because it does not group sequences using external information (e.g. precomputed evolutionary taxonomies), so there is no way to implement what you are suggesting.
More importantly, this is an unbiased test. It would not have been published otherwise.
Why is it so hard to accept this analysis and its conclusions? What I’m presenting here isn’t even in conflict with YEC. Ken Ham thinks that all bacteria are a single “kind,” so maybe they all do share a common ancestor.
I just don’t understand the creativity and persistence of your objections. Are you really confused about this? Or is this really a difficult conclusion to accept? What exactly is supporting your reticence?