And with regards to trying to understand BLAST and VP62, I have written something, that I hope might be helpful:
Let's say hypothetical, that Alice has a fragment of a handwritten book, only a few pages. These pages look like from medieval times, but Alice doesn't know how old the pages are, and is not sure exactly from which book they came from.
So Alice makes a copy of the few pages she has and gives these copies to Bob. Bob has a large database with copies of the content of all handwritten books he could get. To find matching books, he uses eTBLAST If anybody can find out more about the book, then it is Bob.
And Bob looks into his database and the closest match eTBLAST finds are handwritten Bibles from some 13th century monastery in northern Italy. Bob finds that the copies from Alice have a few spelling differences from the copy that is in Bob's database. But Alice copies share all the peculiar spellings that only these 13th Bibles from that northern Italy monastery have.
So Bob is pretty certain that the handwritten pages Alice has were directly transcribed of these 13th century Bibles from that northern Italy monastery. They may have been made later, they may have been made in another place, but it is a direct copy of that Bible, alright. Also, the number spelling differences is very low, so it is most likely a first generation copy.
Yet, Alice says that these pages are not from a Bible, but actually from the Talmud! So Bob asks for some pages that show that these pages came from the Talmud. Alice declines to provide pages that could show that these pages came from the Talmud, but keeps on insisting these pages came from a Talmud copy.
Now, what would you find more closer to reality? Alice's claim that these pages came from the Talmud? Or Bob's analysis that show the relation exactly one sort of Bibles?
(With thanks to Dan Dennett's book "Darwin Dangerous Idea" for giving me the idea – a book, albeit a bit longish, I can only highly recommend for anybody trying to understand some of the basic concepts of evolution)
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