STADEN

Application data
Created by	R.Staden, S.Dear, J.Bonfield, K.Beal, et al.
Principal bioinformatics method(s)	Sequence assembly, Sequence alignment, Visualisation
Technology	Sanger, 454, Illumina
Created at	MRC Laboratory of Molecular Biology, Wellcome Trust Sanger Institute
Maintained?	Yes
Input format(s)	SAM, BAM, FASTA, Experiment Files, ZTR, AB1, SCF
Output format(s)	SAM, FASTA, FASTQ
Software features	Integrated solution
Programming language(s)	C, C++, Tcl, Fortran
Interface type(s)	Desktop GUI
Resource type(s)	Desktop application
Licence	BSD
Operating system(s)	Linux, Windows, Mac OS X, UNIX

Summary: Includes GAP4, GAP5, SPIN, TREV, and numerous smaller tools.

"Error: no local variable "counter" was set." is not a number.

A collection of tools for sequence processing, assembly, editing and analysis.

It is probably best known for Gap4 - a widely used tool for "finishing" sequencing projects. More recently Gap5 has been produced to handle the larger volumes of data that come from modern sequencing instruments. Both are supported for now, until Gap5 matures and acquires more features out of Gap4.

The Spin program performs DNA and protein sequence analysis, replacing the older sip, nip and pip programs from earlier Staden Package releases. Spin also provides a graphical interface to the EMBOSS package. Unfortunately spin is largely unsupported now (please contact us if you have free time).

Links

• STADEN Source code [ edit link ]
• STADEN Homepage [ edit link ]

• Add a Link

References

1. . 2000. Methods Mol Biol
2. . 2002. Bioinformatics
3. . 2002. Bioinformatics
4. . 1992. DNA Sequence
5. . 1991. Nucleic Acids Research
6. . 2010. Bioinformatics
7. . 1984. Nucleic Acids Research
8. . 1982. Nucleic Acids Research
9. . 1995. Nucleic Acids Research
10. . 1995. Nucleic Acids Research
11. . 1996. DNA Sequence
12. . 1998. Nucleic Acids Research

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