[AndrewC]

OK, I've figured out the problem. You're comparing apples and oranges.

Remember I also stated this ---

I also ran the X-linked ribosomal protein. In that analysis the chicken is closer to human than the primates. Go figure.

Query = gi|12653405|gb|AAH00472.1|AAH00472 ribosomal protein S4, X-linked [Homo sapiens] (263 letters)

[Right Wing Professor]

Remember I also stated this ---

I also ran the X-linked ribosomal protein. In that analysis the chicken is closer to human than the primates. Go figure

194 of 194 amino acids are identical on the aligned human/pig sequences. 190 of 194 are identical on the aligned human/chicken sequences. I'm failing to understand how a sequence with four differences is closer than an identical sequence.

[Right Wing Professor]

To expand on my cryptic remark. The macaque and green monkey proteins are 100% identical to human over the aligned sequence. The two chimp proteins and the gorilla protein are rps4y, the y-linked protein. Do you have some other protein in mind?