Software Updates

BioPerl

a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

Mono

an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

ISOLDE

anvi'o

an open-source, community-driven analysis and visualization platform for ‘omics data. Its interactive interface facilitates the management of metagenomic contigs and associated data for automatic or human-guided identification of genome bins and their curation.

DivCon Discovery Suite

a linear-scaling, semiempirical quantum mechanics (SE-QM) program DivCon with the Phenix X-ray refinement engine. Phenix/DivCon does not utilize CIF(s), link restraints and other refinement parameters so there are fewer assumptions about the model. Accurate energy and density scoring tools also allow tautomer/protomer and “flip state” determination.

ChimeraX

a next-generation molecular visualization program, following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface. ChimeraX will have documented programming interfaces and an easy-to-use “Tool Shed” web repository of extensions.

BLAST+

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.