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A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the(More)
Hill-Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive(More)
The McDonald and Kreitman test (MKT) is one of the most powerful and extensively used tests to detect the signature of natural selection at the molecular level. Here, we present the standard and generalized MKT website, a novel website that allows performing MKTs not only for synonymous and nonsynonymous changes, as the test was initially described, but(More)
Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been rearranged differently in several(More)
Polymorphism studies are one of the main research areas of this genomic era. To date, however, no available web server or software package has been designed to automate the process of exploring and estimating nucleotide polymorphism in large DNA databases. Here, we introduce a novel software, PDA, Pipeline Diversity Analysis, that automatically can (i)(More)
MOTIVATION Polymorphism studies are one of the main research areas of this genomic era. To date, however, no comprehensive secondary databases have been designed to provide searchable collections of polymorphic sequences with their associated diversity measures. RESULTS We define a data model for the storage, representation and analysis of genotypic and(More)
The newest genomic advances have uncovered an unprecedented degree of structural variation throughout genomes, with great amounts of data accumulating rapidly. Here we introduce InvFEST (http://invfestdb.uab.cat), a database combining multiple sources of information to generate a complete catalogue of non-redundant human polymorphic inversions. Due to the(More)
MOTIVATION The completion of 168 genome sequences from a single population of Drosophila melanogaster provides a global view of genomic variation and an understanding of the evolutionary forces shaping the patterns of DNA polymorphism and divergence along the genome. RESULTS We present the 'Population Drosophila Browser' (PopDrowser), a new genome browser(More)
Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (DPDB). A new version of the pipeline presented here, PDA(More)
Multi-locus and multi-species nucleotide diversity studies would benefit enormously from a public database encompassing high-quality haplotypic sequences with their associated genetic diversity measures. MamPol, 'Mammalia Polymorphism Database', is a website containing all the well-annotated polymorphic sequences available in GenBank for the Mammalia class(More)