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Introducing the Sequence Analysis module, including importing of sequence data with VCF files, Filtering with Annotation Tracks, Variant Frequency Binning by MAF, and rare variant burden and collapsing methods such as the Combined Multivariate and Collapsing (CMC) Test.
Improvements to the CNAM module, including adding a Wave Detection and Correction analysis method.
Updated the importing capabilities for Affymetrix Files to utilize auto-downloaded marker maps and reference data as well as handle the new Affymetrix Cytogenetics platform.
Added the ability to GPU devices as hardware acceleration to the CNAM module (see Using CNAM Optimal Segmenting).
Expanded the capabilities of annotation tracks visible in the genome browser with the Annotation Track Manager. These tracks are available from the Python API for querying and filtering and can be used in conjunction with spreadsheets to create powerful work-flows.
Added Identity by Descent Estimation, LD Pruning and other Quality Assurance Procedures to the HelixTree and Whole Genome modules.
Many improvements to the Python APIs for SVS, including a much expanded utility to Commands For User Input.

Added support for importing NimbleGen Data Summary Files.
Updated the PLINK PED/MAP, BED/BIM/FAM and TPED/TFAM import to handle non-human genomes.
Added import support for Affymetrix Files.
Built a Genome Browser into the plot viewer for genomic mapped data. The Genome Browser includes default local tracks as well as the ability to add curated network tracks from the Golden Helix, Inc. annotation server.
Within the genome browser, support for switching genomes to other authoritative builds and even other species is supported. Annotation tracks for other species can be added through the network tracks feature. Although many common genome maps are provided, the ability to build custom genome map is provided through multiple routes.
Many small user interface and feature improvements were added to the plotting system.
In the spreadsheet editor, the find/replace functionality now supports regular expressions.
The integrated Python editor had some extra common editor features added to assist in the writing of Python scripts.
A faster, more powerful and more fully featured Runs of Homozygosity analysis method was implemented.
Updated PBAT family based analysis module with proper parameter restrictions, defaults and efficiency improvements.
Support was added for a concurrent license usage model.