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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).

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.

Pregap/Gap4 course
This PDF file contains notes for a full 2-day course on using pregap4 and gap4. The course/data directory contains the data mentioned within the course notes.


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URL: http://www.mrc-lmb.cam.ac.uk/pubseq/documentation.html