MOTIVATION: Dominant markers (DArTs and AFLPs) are commonly used for genetic analysis in the fields of evolutionary genetics, ecology and conservation of genetic resources. The recent prominence of these markers has coincided with renewed interest in detecting the effects of local selection and adaptation at the level of the genome. RESULTS: We present Mcheza, an application for detecting loci under selection based on a well-evaluated F(ST)-outlier method. The application allows robust estimates to be made of model parameters (e.g. genome-wide average, neutral F(ST)), provides data import and export functions, iterative contour smoothing and generation of graphics in an easy to use graphical user interface with a computation engine that supports multicore processors for enhanced performance. Mcheza also provides functionality to mitigate common analytical errors when scanning for loci under selection. AVAILABILITY: Mcheza is freely available under GPL version 3 from http://popgen.eu/soft/mcheza.

MOTIVATION: The evolution of resistance in Plasmodium falciparum malaria against most available treatments is a major global health threat. Population genetics approaches are commonly used to model the spread of drug resistance. Due to uncommon features in malaria biology, existing forward-time population genetics simulators cannot suitably model Plasmodium falciparum malaria. RESULTS: Here we present ogaraK, a population genetics simulator for modelling the spread of drug-resistant malaria. OgaraK is designed to make malaria simulation computationally tractable as it models infections, not individual parasites. OgaraK is also able to model the life cycle of the parasite which includes both haploid and diploid phases and sexual and asexual reproduction. We also allow for the simulation of different inbreeding levels, an important difference between high and low transmission areas and a fundamental factor influencing the outcome of strategies to control or eliminate malaria. AVAILABILITY: OgaraK is available as free software (GPL) from the address http://popgen.eu/soft/ogaraK.

BACKGROUND: The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This important database does not provide any programmatic access to the dataset, furthermore no standard relational database interface is provided. RESULTS: interPopula is a Python API to access the HapMap dataset. interPopula provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relevant human population datasets (e.g. Ensembl gene annotation and UCSC Known Genes). A set of guidelines and code examples to address possible inconsistencies across heterogeneous data sources is also provided. CONCLUSIONS: interPopula is a straightforward and flexible Python API that facilitates the construction of scripts and applications that require access to the HapMap dataset.

Abstract Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected].

BACKGROUND: Testing for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many non-trivial, error-prone tasks to the user. RESULTS: Here we present LOSITAN, a selection detection workbench based on a well evaluated Fst-outlier detection method. LOSITAN greatly facilitates correct approximation of model parameters (e.g., genome-wide average, neutral Fst), provides data import and export functions, iterative contour smoothing and generation of graphics in a easy to use graphical user interface. LOSITAN is able to use modern multi-core processor architectures by locally parallelizing fdist, reducing computation time by half in current dual core machines and with almost linear performance gains in machines with more cores. CONCLUSION: LOSITAN makes selection detection feasible to a much wider range of users, even for large population genomic datasets, by both providing an easy to use interface and essential functionality to complete the whole selection detection process.

UNLABELLED: MODELER4SIMCOAL2 (M4S2) is an extensible graphical tool to model linked loci and population demographies. M4S2 is easy to use, allowing for the modeling of complicated scenarios, making coalescent simulation modeling accessible to biologists with limited computer skills. The software includes an extension system allowing for new models to be created, published and downloaded from the Internet. AVAILABILITY: M4S2 is available from http://popgen.eu/soft/m4s2 under a GPL license. The web site also contains guides, screen shots and tutorials.