This script is for Slackware 13.37 only and may be outdated.

SlackBuilds Repository

13.37 > Academic > staden (2.0.0b9)

The programs part of the Staden package provide a 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
GAP5 - The new development version of Gap4, designed to work with the
large volumes of data attainable through the newer sequencing
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.

This requires io_lib and tklib.

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.

Maintained by: Petar Petrov
Keywords: staden,staden package,io_lib,bioinformatics,biology,science,sequence analysis
ChangeLog: staden


Source Downloads:
tcl8.5.9-src.tar.xz (c1e4eea4afdd9a8f8888d5b7c481122d)
staden-2.0.0b9-src.tar.gz (94dc304b00d18b95f783136c9ffd934f)
staden_doc-2.0.0b9-src.tar.gz (730b433d8344624925b662ec37ac0804)
tk8.5.9-src.tar.xz (78b59df55904095af40d64a0cd08c50d)

Download SlackBuild:
staden.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Individual Files:

Validated for Slackware 13.37

See our HOWTO for instructions on how to use the contents of this repository.

Access to the repository is available via:
ftp git cgit http rsync

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