The Staden Package
The staden package
https://staden.sf.net
DNA sequence assembly (Gap4/Gap5), editing and analysis tools
Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin).
Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy.
Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes.
Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.
Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project.
Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4.
Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix analysis, global and local alignment algorithms, plus a sliding sequence window linked to the graphical plots. It can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid.
Licensing
License
Verified by
Verified on
Notes
License
Verified by
Debian: Sergei Golovan <sgolovan@debian.org>
Verified on
11 July 2014
Notes
License: tcltk
TclTk This text was blatantly stolen from Tcl/Tk license and adapted - thus assume it falls under similar license terms.
The authors hereby grant permission to use, copy, modify, distribute, and license this software and its documentation for any purpose, provided that existing copyright notices are retained in all copies and that this notice is included verbatim in any distributions. No written agreement, license, or royalty fee is required for any of the authorized uses.
IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON- INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
RESTRICTED RIGHTS: Use, duplication or disclosure by the U.S. government is subject to the restrictions as set forth in subparagraph (c) (1) (ii) of the Rights in Technical Data and Computer Software Clause as DFARS 252.227-7013 and FAR 52.227-19.
SPECIAL NOTES:
This software is also falls under the bourbon_ware clause:
Should you find this software useful in your daily work, you should feel obliged to take the author out for a drink if the opportunity presents itself. The user may feel exempt from this clause if they are under 21 or think the author has
already partaken of too many drinks.License
Verified by
Debian: Sergei Golovan <sgolovan@debian.org>
Verified on
11 July 2014
Notes
License: bsd-like
License
Verified by
Debian: Sergei Golovan <sgolovan@debian.org>
Verified on
11 July 2014
Notes
License: permission_granted
permission_granted Permission to use, copy, modify and distribute this software and its documentation for any purpose is hereby granted without fee, provided that this copyright and notice appears in all copies.
This file was written as part of the Staden Package at the MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
MRC disclaims all warranties with regard to this software.License
Verified by
Debian: Sergei Golovan <sgolovan@debian.org>
Verified on
11 July 2014
Notes
License: bsd-primer3
BSD-primer3 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Redistributions of source code must also reproduce this information in the source code itself.
2. If the program is modified, redistributions must include a notice (in the same places as above) indicating that the redistributed program is not identical to the version distributed by Whitehead Institute.
3. All advertising materials mentioning features or use of this software must display the following acknowledgment: This product includes software developed by the Whitehead Institute for Biomedical Research.
4. The name of the Whitehead Institute may not be used to endorse or promote products derived from this software without specific prior written permission.
We also request that use of this software be cited in publications as
Steve Rozen, Helen J. Skaletsky (1996,1997,1998) Primer3. Code available at http://www- genome.wi.mit.edu/genome_software/other/primer3.html
THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.License
Verified by
Debian: Sergei Golovan <sgolovan@debian.org>
Verified on
11 July 2014
Notes
License: uc_sun_scriptics
Leaders and contributors
| Contact(s) | Role |
|---|---|
| http://sourceforge.net/p/staden/bugs/ | contact |
Resources and communication
| Audience | Resource type | URI |
|---|---|---|
| Debian (Ref) (R) | https://tracker.debian.org/pkg/staden | |
| Download | http://sourceforge.net/projects/staden/files/ |
Software prerequisites
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.
The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.