02376nas a2200289   4500008004100000022001400041245012000055210006900175260001300244300001000257490000700267520143700274653001201711653002301723653002501746653002101771653002001792653001101812653001101823653000901834653002201843100002401865700002001889700002301909700002001932856013401952       2011                        eng d  a1477-405400aEvidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.0 aEvidence for shorttime divergence and longtime conservation of t  c2011 Sep  a442-80 v123 a<p>Gene duplication is one of the main mechanisms by which genomes can acquire novel functions. It has been proposed that the retention of gene duplicates can be associated to processes of tissue expression divergence. These models predict that acquisition of divergent expression patterns should be acquired shortly after the duplication, and that larger divergence in tissue expression would be expected for paralogs, as compared to orthologs of a similar age. Many studies have shown that gene duplicates tend to have divergent expression patterns and that gene family expansions are associated with high levels of tissue specificity. However, the timeframe in which these processes occur have rarely been investigated in detail, particularly in vertebrates, and most analyses do not include direct comparisons of orthologs as a baseline for the expected levels of tissue specificity in absence of duplications. To assess the specific contribution of duplications to expression divergence, we combine here phylogenetic analyses and expression data from human and mouse. In particular, we study differences in spatial expression among human-mouse paralogs, specifically duplicated after the radiation of mammals, and compare them to pairs of orthologs in the same species. Our results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event.</p>10aAnimals10aConserved Sequence10aEvolution, Molecular10aGene Duplication10agene expression10aGenome10aHumans10aMice10aOrgan Specificity1 aHuerta-Cepas, Jaime1 aDopazo, Joaquin1 aHuynen, Martijn, A1 aGabaldón, Toni  uhttps://www.clinbioinfosspa.es/content/evidence-short-time-divergence-and-long-time-conservation-tissue-specific-expression-after02025nas a2200349   4500008004100000022001400041245011700055210006900172260001300241300001100254490000700265520090400272653002501176653001301201653001301214653001401227653002301241653001301264100002101277700002101298700002301319700002001342700002101362700001701383700002401400700003301424700002401457700002001481700002001501700002001521856013401541       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  uhttps://www.clinbioinfosspa.es/content/phylemon-20-suite-web-tools-molecular-evolution-phylogenetics-phylogenomics-and-hypotheses02514nas a2200217   4500008004100000022001400041245005200055210005000107260001600157300000700173490000700180520188600187653002602073653002302099653001402122653001302136100002402149700002002173700002002193856008302213       2010                        eng d  a1471-210500aETE: a python Environment for Tree Exploration.0 aETE a python Environment for Tree Exploration  c2010 Jan 13  a240 v113 a<p><b>BACKGROUND: </b>Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale.</p><p><b>RESULTS: </b>Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations.</p><p><b>CONCLUSIONS: </b>ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.</p>10aComputational Biology10aDatabases, Genetic10aPhylogeny10aSoftware1 aHuerta-Cepas, Jaime1 aDopazo, Joaquin1 aGabaldón, Toni  uhttps://www.clinbioinfosspa.es/content/ete-python-environment-tree-exploration03102nas a2200325   4500008004100000245012300041210006900164260001600233520197300249100001902222700001902241700002402260700002102284700001702305700003102322700002002353700003002373700002502403700002402428700001902452700001902471700002102490700002602511700002402537700002902561700001802590700002002608700001902628856012902647       2010                        eng d00aFine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.0 aFinescale evolution genomic phenotypic and ecological differenti  c2010 Feb 183 a<p>Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.The ISME Journal advance online publication, 18 February 2010; doi:10.1038/ismej.2010.6.</p>1 aPeña, Arantxa1 aTeeling, Hanno1 aHuerta-Cepas, Jaime1 aSantos, Fernando1 aYarza, Pablo1 aBrito-Echeverría, Jocelyn1 aLucio, Marianna1 aSchmitt-Kopplin, Philippe1 aMeseguer, Inmaculada1 aSchenowitz, Chantal1 aDossat, Carole1 aBarbe, Valerie1 aDopazo, Joaquín1 aRosselló-Mora, Ramon1 aSchüler, Margarete1 aGlöckner, Frank, Oliver1 aAmann, Rudolf1 aGabaldón, Toni1 aAntón, Josefa  uhttps://www.clinbioinfosspa.es/content/fine-scale-evolution-genomic-phenotypic-and-ecological-differentiation-two-coexisting02130nas a2200301   4500008004100000022001400041245007500055210006900130260001300199300001100212490000700223520123800230653001801468653002101486653001001507653001301517653002101530653001101551653001401562653001301576653002901589653002301618100002401641700001801665700002001683700002001703856010501723       2008                        eng d  a1362-496200aPhylomeDB: a database for genome-wide collections of gene phylogenies.0 aPhylomeDB a database for genomewide collections of gene phylogen  c2008 Jan  aD491-60 v363 a<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>10aBase Sequence10aEscherichia coli10aGenes10aGenomics10aHistory, Ancient10aHumans10aPhylogeny10aProteins10aSaccharomyces cerevisiae10aSequence Alignment1 aHuerta-Cepas, Jaime1 aBueno, Anibal1 aDopazo, Joaquin1 aGabaldón, Toni  uhttps://www.clinbioinfosspa.es/content/phylomedb-database-genome-wide-collections-gene-phylogenies-0