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Contents of README:The programs part of the Staden package provide an excellent and fully developed set of DNA sequence assembly, editing, analysis and more. Some of its features include: GAP4 - Performs assembly, contig joining, assembly checking, repeat search, experiment suggestion, read pair analysis and contig editing. GAP5 - The new development version of Gap4, designed to work with the large volumes of data attainable through the newer sequencing technologies. PREGAP4 - Provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis. SPIN - Compares pairs of sequences in many ways, often presenting its results graphically and has a sliding sequence window linked to the plots. TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF trace files. For more information and citing, visit Staden's web page and check the "References" file in the documentation. Notes: 1) You should run the SlackBuild in real root environment (su -)! 2) Make sure you have Emacs and Tetex installed at build time. 3) Although unsupported at the moment, SPIN can provide a GUI for the EMBOSS suite programs. If you want to give it a try, run as root "create_emboss_data" (EMBOSS should be installed, of course). This generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl, so remember to manually clean them if you later uninstall staden. |
Name Last modified Size
Parent Directory - desktop/ 10-Jun-2022 19:27 - README 29-Sep-2012 06:34 1.4K References 23-Dec-2011 00:00 9.1K doinst.sh 23-Dec-2011 17:27 129 slack-desc 23-Dec-2011 17:27 781 staden.SlackBuild 07-Oct-2012 18:14 5.8K staden.info 29-Sep-2012 06:34 741
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