academic/staden/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 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.

NOTE: Xfce submenus
For XFCE, if you want to have the menu entries grouped in a submenu
folder (multilevel menu entry), do:

  SUBMENU="YES" ./staden.SlackBuild

NOTE: Staden and EMBOSS:
Staden used to provide a GUI for (at least part of) the programs from
EMBOSS. To give it a try, run this after install (of course you need to
have installed EMBOSS, too):

  create_emboss_files

This will create some files in:

  /usr/share/staden/tcl/spin_emboss/acdtcl/

CITING
For more information and citing, visit Staden's web page and check the
"References" file in the documentation.