Motivation: Advances in sequencing technologies have made it feasible to obtain massive datasets for phylogenomic inference, often consisting of large numbers of loci from multiple species and individuals. The phylogenomic analysis of next-generation sequencing (NGS) data requires a complex computational pipeline where multiple technical and methodological decisions are necessary that can influence the final tree obtained, like those related to coverage, assembly, mapping, variant calling and/or phasing. Results: To assess the influence of these variables we introduce NGSphy, an open-source tool for the simulation of Illumina reads/read counts obtained from haploid/diploid individual genomes with thousands of independent gene families evolving under a common species tree. In order to resemble real NGS experiments, NGSphy includes multiple options to model sequencing coverage (depth) heterogeneity across species, individuals and loci, including off-target or uncaptured loci. For comprehensive simulations covering multiple evolutionary scenarios, parameter values for the different replicates can be sampled from user-defined statistical distributions. Availability and implementation: Source code, full documentation and tutorials including a 'Getting started' guide are available at http://github.com/merlyescalona/ngsphy. Supplementary information: Supplementary data are available at Bioinformatics online.

Physicians are faced with questions and uncertainties regarding information/knowledge for the best care of their patients. There are several sources of medical information available from which they can retrieve the necessary answers, such as colleagues, textbooks or software on personal digital assistants (PDA). This case study evaluates how physicians seek medical knowledge when they face a clinical challenge. Our observational study took place in one of the US Veterans Affair (VA) Hospitals, during August 2006, with combined observation of, and interviews with, physicians. Search for information was significantly different in strategy and materials used depending on location, temporality and complexity of the question.