@article {17567924,
	title = {The human phylome},
	journal = {Genome Biol},
	volume = {8},
	number = {6},
	year = {2007},
	note = {Huerta-Cepas, Jaime Dopazo, Hernan Dopazo, Joaquin Gabaldon, Toni Research Support, Non-U.S. Gov{\textquoteright}t England Genome biology Genome Biol. 2007;8(6):R109.},
	pages = {R109},
	abstract = {BACKGROUND: Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them. RESULTS: We reconstruct here the human phylome, which includes the evolutionary relationships of all human proteins and their homologs among 39 fully sequenced eukaryotes. Phylogenetic techniques used include alignment trimming, branch length optimization, evolutionary model testing and maximum likelihood and Bayesian methods. Although differences with alternative topologies are minor, most of the trees support the Coelomata and Unikont hypotheses as well as the grouping of primates with laurasatheria to the exclusion of rodents. We assess the extent of gene duplication events and their relationship with the functional roles of the protein families involved. We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation. Using a novel algorithm that is independent from a species phylogeny, we derive orthology and paralogy relationships of human proteins among eukaryotic genomes. CONCLUSION: Topological variations among phylogenies for different genes are to be expected, highlighting the danger of gene-sampling effects in phylogenomic analyses. Several links can be established between the functions of gene families duplicated at certain phylogenetic splits and major evolutionary transitions in those lineages. The pipeline implemented here can be easily adapted for use in other organisms.},
	keywords = {Animals *Evolution Evolution, DNA, Molecular Gene Duplication *Genome Humans *Phylogeny Proteins/genetics Sequence Analysis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17567924},
	author = {Huerta-Cepas, J. and H. Dopazo and Dopazo, J. and Gabald{\'o}n, T.}
}
@article {11442348,
	title = {Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate},
	journal = {Microb Drug Resist},
	volume = {7},
	number = {2},
	year = {2001},
	note = {Dopazo, J Mendoza, A Herrero, J Caldara, F Humbert, Y Friedli, L Guerrier, M Grand-Schenk, E Gandin, C de Francesco, M Polissi, A Buell, G Feger, G Garcia, E Peitsch, M Garcia-Bustos, J F United States Microbial drug resistance (Larchmont, N.Y.) Microb Drug Resist. 2001 Summer;7(2):99-125.},
	pages = {99-125},
	abstract = {The public availability of numerous microbial genomes is enabling the analysis of bacterial biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope. Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the world. We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA, covering more than 90\% of the total estimated size of the genome. The sequenced strain is a clinical isolate resistant to macrolides and tetracycline. It carries a type 19F capsular locus, but multilocus sequence typing for several conserved genetic loci suggests that the strain sequenced belongs to a pneumococcal lineage that most often expresses a serotype 15 capsular polysaccharide. A total of 2,046 putative open reading frames (ORFs) longer than 100 amino acids were identified (average of 1,009 bp per ORF), including all described two-component systems and aminoacyl tRNA synthetases. Comparisons to other complete, or nearly complete, bacterial genomes were made and are presented in a graphical form for all the predicted proteins.},
	keywords = {Bacterial Molecular Sequence Data Pneumococcal Infections/*microbiology Prokaryotic Cells RNA, Bacterial/chemistry/genetics Genes, Bacterial/genetics *Genome, DNA, Transfer/metabolism Streptococcus pneumoniae/*genetics},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=11442348},
	author = {Dopazo, J. and Mendoza, A. and Herrero, J. and Caldara, F. and Humbert, Y. and Friedli, L. and Guerrier, M. and Grand-Schenk, E. and Gandin, C. and de Francesco, M. and Polissi, A. and Buell, G. and Feger, G. and Garcia, E. and Peitsch, M. and Garcia-Bustos, J. F.}
}
