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GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis too...

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been...

Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes cal...

BACKGROUND: RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issu...

Phylogenies are extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their parts (e.g. genes), but also for a variety of research once the phylogenies are estimated. ...

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cg...

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for informatio...

One of the frequent questions by users of the mixed model function lmer of the lme4 package has been: How can I get p values for the F and t tests for objects returned by lmer? The lmerTest package extends the 'lmerMod' ...

The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

Materias / palabras clave: computer science, omics, software tools, computational methods, datasets; Science: Mathematics: Instruments and machines: Electronic computers. Computer science

Materias / palabras clave: molecular biology, biotechnology, medical informatics, software tools, databases, data integration; Technology: Chemical technology: Biotechnology

Materias / palabras clave: software tools and applications, applied electromagnetics and electronics, signal processing and multimedia, telecommunications networks, radio communications, communications systems; Technology: Electrical engineering. ...

Materias / palabras clave: information technology and systems, pattern thinking, knowledge processing methods and tools, mathematical modeling, computer engineering and software; Technology: Electrical engineering. Electronics. Nuclear engineering...