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.

Old manuals

The old package manual from version 1994.2. This is documentation for the older programs, such as nip (not nip4) and pip. This is not being updated, so look in the current manual first for information. The manual may also be downloaded from our ftp site.