@article {539,
	title = {Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.},
	journal = {Nucleic Acids Res},
	volume = {39},
	year = {2011},
	month = {2011 Jul},
	pages = {W470-4},
	abstract = {<p>Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.</p>},
	keywords = {Evolution, Molecular, Genomics, Internet, Phylogeny, Sequence Alignment, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkr408},
	author = {S{\'a}nchez, Rub{\'e}n and Serra, Fran{\c c}ois and T{\'a}rraga, Joaqu{\'\i}n and Medina, Ignacio and Carbonell, Jos{\'e} and Pulido, Luis and De Maria, Alejandro and Capella-Gut{\'\i}errez, Salvador and Huerta-Cepas, Jaime and Gabald{\'o}n, Toni and Dopazo, Joaquin and Dopazo, Hern{\'a}n}
}
@article {598,
	title = {PhylomeDB: a database for genome-wide collections of gene phylogenies.},
	journal = {Nucleic Acids Res},
	volume = {36},
	year = {2008},
	month = {2008 Jan},
	pages = {D491-6},
	abstract = {<p>The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.es.</p>},
	keywords = {Base Sequence, Escherichia coli, Genes, Genomics, History, Ancient, Humans, Phylogeny, Proteins, Saccharomyces cerevisiae, Sequence Alignment},
	issn = {1362-4962},
	doi = {10.1093/nar/gkm899},
	author = {Huerta-Cepas, Jaime and Bueno, Anibal and Dopazo, Joaquin and Gabald{\'o}n, Toni}
}
