The 1.6.0 release of the Staden Package has finally been made available. For full details see the release notes.
The latest build of the Staden Package is well under way. A beta-test version of the Windows release has been made available. Other platforms to follow shortly.
The biggest change is to allow Gap4 to handle 64-bit file sizes. Practically this means that very large assembly databases can be worked on (tested with ~2.6 million readings). There's a whole host of speedups associated with this too.
There's also a new experimental "SNP candidates" plot designed to identify places where we may have a population rather than a single sequence (such as a collapsed repeat or simply variations in a diploid assembly). By correlating the differences the sequences can be broken down into sets and either visualised in the contig editor or broken apart to new contigs.
For downloads, please visit the SourceForge files section.
A new version of the sequence chromatogram (trace) I/Ol library has been made available. The primary change is for speed. This has been achieved by doing most encoding and decoding in memory instead of on-disk, but this comes at the expense of incompatibility in some of the more low-level functions.
Full details can be found in the release notes
It can be downloaded from here.