Research / Software. Manipulation of input and output files related to whole-genome shotgun assembly. Currently maintained at CBCB at the University of Maryland. CABOG assembles long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. DNA Barcode Deconvolution This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid.
Elvira High throughput assembly of amplicon reads for virus-sized genomes. Lucy A tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses. TIGR Assembler Enabled the first published whole-genome assembly of a free-living organism in 1995. Middleware for organizing large chunks of data to free the client from having to encode data storage specifics. Glimmer A microbial gene-finding system, especially in bacteria, archaea, and viruses. A tool for analyzing and annotating eukaryotic genomic sequences. Manatee ANDES Tools. ApE- A plasmid Editor. Gatekeeper will report that the application is damaged and will prevent ApE from running.
You have to go to System Preferences > Security and Privacy > General. Check "Allow software downloaded from anywhere" to allow ApE to run. Appearntly, right click on ApE and select "Open" will not work to bypass Gatekeeper on all systems. Or use a command line function to change the quarantine attributes. I may need to put ApE on the Apple store and start charging for it to get around this in the future. The current Mac version has a bad bug on Mavericks. Click here to make a voluntary donation in support of ApE. Get older versions Click the icons at the top of the page for the latest version (version 2.0.x is out of alpha testing) You can now export genomic regions from Wormbase directly: In the upper right drop-down menu button, select "Download Track Data".
Alternatively, you can export a genomic region (from the genome viewer) as a FASTA formatted file (using the menu on the upper left). GenoCAD: CAD Software for Synthetic Biology. Serial Cloner. Download | Utopia.