OpenEye has released OpenEye Toolkits v2012.Oct.
This release includes the C++, Python, and .NET versions of several toolkits.
The full release notes are available here.
The toolkits can be downloaded here.
Release 16 of Ensembl Genomes is available here.
The release includes a migration to version 69 of the Ensembl software; the addition of several new species in Ensembl plants and Ensembl metazoan; improvements to the wheat assembly; and the ability to highlight annotations in gene trees among other updates.
Bowtie 2 2.0.1 is available here.
The release fixes several bugs as well as an issue that would cause Bowtie 2 to use excessive amounts of memory for closely matching and highly repetitive reads under some circumstances, among other improvements.