Package: staden (2.0.0+b11-5 and others)

[ Source: staden  ]

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.

Other Packages Related to staden

• dep: libbz2-1.0 [sparc64]

  고성능 블럭 소팅 파일 압축 라이브러리 - 런타임

• dep: libc6 (>= 2.29) [hppa]

  GNU C 라이브러리: 공유 라이브러리
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.34) [not alpha, arm64, hppa, ia64, loong64, sh4]

  dep: libc6 (>= 2.37) [loong64, sh4]

  dep: libc6 (>= 2.38) [arm64]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C 라이브러리: 공유 라이브러리
  also a virtual package provided by libc6.1-udeb

  dep: libc6.1 (>= 2.37) [ia64]

• dep: libcurl3-gnutls (>= 7.16.2) [hppa]

  사용하기 쉬운 클라이언트측 URL 전송 라이브러리 (GnuTLS 지원)

• dep: libcurl3t64-gnutls (>= 7.16.2) [sparc64]

  사용하기 쉬운 클라이언트측 URL 전송 라이브러리 (GnuTLS 지원)

• dep: libfontconfig1 (>= 2.12.6) [hppa, sparc64]

  일반 글꼴 설정 라이브러리 - 런타임

• dep: libfreetype6 (>= 2.2.1) [hppa, sparc64]

  FreeType 2 font engine, shared library files

• dep: libgcc-s1 (>= 3.0) [not armel, armhf, hppa, ia64, m68k, sh4]

  GCC 기능 지원 라이브러리

  dep: libgcc-s1 (>= 3.3.4) [sh4]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC 기능 지원 라이브러리

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC 기능 지원 라이브러리

• dep: liblzma5 (>= 5.1.1alpha+20120614)

  XZ 형식 압축 라이브러리

• dep: libpng16-16 (>= 1.6.2-1) [hppa]

  PNG library - runtime (version 1.6)

• dep: libpng16-16t64 (>= 1.6.2) [not hppa]

  PNG library - runtime (version 1.6)

• dep: libstaden-read14 (>= 1.14.12) [hppa]

  Staden library for reading and writing DNA sequencing results

• dep: libstaden-read14t64 (>= 1.14.12) [not hppa]

  Staden library for reading and writing DNA sequencing results

• dep: libstdc++6 (>= 5)

  GNU 표준 C++ 라이브러리 v3

• dep: libtcl8.6 (>= 8.6.0)

  Tcl (Tool Command Language) v8.6 - 런타임 라이브러리 파일들

• dep: libtk8.6 (>= 8.6.0)

  Tk toolkit for Tcl and X11 v8.6 - run-time files

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: libx11-6

  X11 client-side library

• dep: libxext6 [hppa, sparc64]

  X11 다양한 확장 라이브러리

• dep: libxft2 (>> 2.1.1) [hppa, sparc64]

  X에 대한 FreeType 기반 폰트 드로잉 라이브러리

• dep: libxss1 [hppa, sparc64]

  X11 Screen Saver extension library

• dep: staden-common (= 2.0.0+b11-4) [hppa]

  Architecture independent files for Staden

  dep: staden-common (= 2.0.0+b11-5) [not hppa]

• dep: staden-io-lib-utils

  programs for manipulating DNA sequencing files

• dep: tklib

  standard Tk Library

• dep: zlib1g (>= 1:1.1.4) [not armel, armhf, m68k, sh4]

  압축 라이브러리 - 런타임

  dep: zlib1g (>= 1:1.2.3.4) [armel, armhf, m68k, sh4]

• rec: med-config [not hppa]

  Debian Med 일반 구성 패키지

  rec: med-config (>= 2.1) [hppa]

Download staden

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.0.0+b11-5	1,591.3 kB	6,513.0 kB	[list of files]
amd64	2.0.0+b11-5	1,606.2 kB	4,722.0 kB	[list of files]
arm64	2.0.0+b11-5+b1	1,494.0 kB	6,023.0 kB	[list of files]
armel	2.0.0+b11-5	1,374.9 kB	4,108.0 kB	[list of files]
armhf	2.0.0+b11-5	1,387.3 kB	3,100.0 kB	[list of files]
hppa (unofficial port)	2.0.0+b11-4+b1	1,578.2 kB	4,879.0 kB	[list of files]
i386	2.0.0+b11-5	1,692.4 kB	5,122.0 kB	[list of files]
ia64 (unofficial port)	2.0.0+b11-5	1,918.2 kB	8,376.0 kB	[list of files]
loong64 (unofficial port)	2.0.0+b11-5	1,537.5 kB	4,976.0 kB	[list of files]
m68k (unofficial port)	2.0.0+b11-5	1,398.5 kB	4,087.0 kB	[list of files]
mips64el	2.0.0+b11-5	1,417.6 kB	6,272.0 kB	[list of files]
ppc64 (unofficial port)	2.0.0+b11-5	1,695.9 kB	7,621.0 kB	[list of files]
ppc64el	2.0.0+b11-5	1,721.0 kB	7,045.0 kB	[list of files]
riscv64	2.0.0+b11-5	1,624.9 kB	3,991.0 kB	[list of files]
s390x	2.0.0+b11-5	1,622.5 kB	5,006.0 kB	[list of files]
sh4 (unofficial port)	2.0.0+b11-5	1,725.8 kB	5,263.0 kB	[list of files]
sparc64 (unofficial port)	2.0.0+b11-5	1,514.0 kB	35,433.0 kB	[list of files]
x32 (unofficial port)	2.0.0+b11-5	1,598.2 kB	4,427.0 kB	[list of files]