02020nas a2200349   4500008004100000022001400041245011700055210006900172260001300241300001100254490000700265520090400272653002501176653001301201653001301214653001401227653002301241653001301264100002101277700002101298700002301319700002001342700002101362700001701383700002401400700003301424700002401457700002001481700002001501700002001521856012901541       2011                        eng d  a1362-496200aPhylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.0 aPhylemon 20 a suite of webtools for molecular evolution phylogen  c2011 Jul  aW470-40 v393 a<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>10aEvolution, Molecular10aGenomics10aInternet10aPhylogeny10aSequence Alignment10aSoftware1 aSánchez, Rubén1 aSerra, François1 aTárraga, Joaquín1 aMedina, Ignacio1 aCarbonell, José1 aPulido, Luis1 aDe Maria, Alejandro1 aCapella-Gutíerrez, Salvador1 aHuerta-Cepas, Jaime1 aGabaldón, Toni1 aDopazo, Joaquin1 aDopazo, Hernán  uhttp://clinbioinfosspa.es/content/phylemon-20-suite-web-tools-molecular-evolution-phylogenetics-phylogenomics-and-hypotheses02554nas a2200361   4500008004100000245014100041210006900182260001600251300003100267490000700298520145100305653001501756653002001771653001501791653001001806653000801816653000901824100002001833700002101853700001701874700002101891700001801912700001601930700002301946700002901969700002701998700002002025700002302045700002002068700002002088700002102108856006302129       2010                        eng d00aBabelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.0 aBabelomics an integrative platform for the analysis of transcrip  c2010 May 16  aW210-W213. Featured in NAR0 v383 a<p>Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data analysis facilities are integrated and connected to multiple options for the functional interpretation of the experiments. Different methods of functional enrichment or gene set enrichment can be used to understand the functional basis of the experiment analyzed. Many sources of biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein-protein interaction modules can be used for this purpose. Finally a tool for the de novo functional annotation of sequences has been included in the system. This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org.</p>10ababelomics10agene expression10agenotyping10agepas10aGSA10aGWAS1 aMedina, Ignacio1 aCarbonell, José1 aPulido, Luis1 aMadeira, Sara, C1 aGoetz, Stefan1 aConesa, Ana1 aTárraga, Joaquín1 aPascual-Montano, Alberto1 aNogales-Cadenas, Ruben1 aSantoyo, Javier1 aGarcía, Francisco1 aMarbà, Martina1 aMontaner, David1 aDopazo, Joaquín  uhttp://nar.oxfordjournals.org/content/38/suppl_2/W210.full