Phylogenomics can be regarded as the intersection between the fields of evolution and genomics[1]. The term has been used in multiple ways to refer to some type of analysis involving genome data and evolutionary reconstructions, especially phylogenetics. Examples of different flavors of phylogenomics include:
Prediction of the function of a gene based on its evolutionary history in a phylogenetic tree. This was the original use of the term [2][3]. For reviews of this aspect of phylogenomics see [4][5]
Reconstruction of a species tree by combining the information from many genes or entire genomes [6][7][8]
The integration of genome analysis and evolutionary reconstruction [9][10]
^ Eisen JA, Kaiser D, Myers RL. 1997. Gastrogenomic delights: a movable feast. Nat Med. 3(10):1076-8. PMID 9334711
^ Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8(3):163-7. PMID 9521918
^ Brown D, Sjölander K. Functional classification using phylogenomic inference. PLoS Comput Biol. 2006 Jun 30;2(6):e77. PMID 16846248
^ Sjölander K. Bioinformatics. 2004 Jan 22;20(2):170-9. Phylogenomic inference of protein molecular function: advances and challenges. PMID 14734307
^ Delsuc F, Brinkmann H, Philippe H.Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005 6(5):361-75.
^ Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D. Mol Biol Evol. 2004 Sep;21(9):1740-52. Phylogenomics of eukaryotes: impact of missing data on large alignments.
^ Jeffroy O, Brinkmann H, Delsuc F, Philippe H. Phylogenomics: the beginning of incongruence? Trends Genet. 2006 Apr;22(4):225-31. PMID 16490279
^ Eisen JA, Fraser CM. Phylogenomics: intersection of evolution and genomics. Science. 2003 Jun 13;300(5626):1706-7. PMID 12805538
^ Eisen JA, Hanawalt PC. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res. 1999 Dec 7;435(3):171-213. PMID 10606811
