Documentation

Release notes: Links to the release notes for each package release.
Program summary: A chart of the various program names and brief descriptions. Also makes a handy documentation finder.
User Manual: Online documentation for the more recent programs, including. File formats, Gap4, Trev and Spin. This documentation forms the basis of the printed manual as well as online help and manual pages.
Mini Manual: A cut down version of the manual to give an introduction to the main programs in the package (around 45 pages when printed).
Mutation detection methods: This document provides a summary of the mutation detection methods included within the package. It consists of a brief guide, with screen shots, covering the key details. A more detailed set of "course notes" are being prepared to cover mutation detection.
Phrap and Gap4 integration: This describes modifications to Phrap to allow it to work with Experiment Files. This, coupled with a Phrap assembly menu in Gap4 gives easy integration. Additionally new editing features make problem detection faster and consensus generation more reliable.
References and papers: A list of references about the package. This also includes, when permissable, copies of the papers themselves.
Programming manual: This contains documentation on the Tcl interfaces to gap4 and methods of building your own plug-in packages to extend gap4. This, the first draft, deals primarily with Gap4.
Definition of a Contig: Due to there being so many conflicting definitions of the term "contig" in use, this page describes the original definition. It is also the definition used by the Staden Package.
Scramble / CRAM benchmarks: Multi-threading benchmarks of CRAM when produced by io_lib's Scramble tool. Comparisons are made to a variety of other related tools and file formats.