文档介绍：Journal of Systematics and Evolution 46 (3): 258–262 (2008) doi: .
(formerly Acta Phynd phylogeny, has been quite ism. We use the NCBI curated RefSeq (Pruitt et al.,
limited. No wonder merely a few years ago Carl 2007) sequences in order to provide a common basis
Woese called microbiology “the science without a of comparison. Then the number of K-peptides is
past” (Woese, 2000). Nevertheless, the use of 16S counted by using a sliding window, shifting one letter
rRNA sequences to infer prokaryotic phylogeny, at a time along all protein sequences. These counts are
suggested by Woese and collaborators (Woese & Fox, kept in a fixed lexicographic order of amino acid
1977), has brought about a wealth of new knowledge. letters to form a vector with 20K components. A key
As a consequence of this success, the modern pro- procedure leading to the final composition vector is
karyotic taxonomy as reflected in the new edition of the subtraction of a background caused mainly by
Bergey’s Manual of Systematic Bacteriology (Ber- neutral mutations in order to highlight the shaping role
gey’s Manual Trust, 2001–2009) is now largely based of natural selection. As mutations occur randomly at
on 16S rRNA analysis. This situation, however, molecular level (Kimura, 1983), this is done by using
broaches a question of principle: the Bergey’s tax