Reply To Li Et Al.: Organism Tree Of Life: Gene Phylogeny Vs. Whole-Proteome Phylogeny

In responding to the Letter by Li et al. (1) regarding our paper (2), we would like to remind the authors of the Letter that 1) the concept and structure of organism tree of life (“organism ToL”) have been evolving since Darwin’s time and are expected to continue to evolve as the types and amounts of genomic data increase, as well as the methods of analyzing the data and constructing the ToL improve; and 2) as a surrogate for the organism ToL, we use whole-proteome sequences (predicted by all protein coding genes) to construct “whole-proteome ToL” in contrast to the commonly used “gene ToLs.” The former uses … \n\n[↵][1]1To whom correspondence may be addressed. Email: sunghou{at}berkeley.edu.\n\n [1]: #xref-corresp-1-1