Package: gff2aplot (2.0-6 and others)

[ Source: gff2aplot  ]

pair-wise alignment-plots for genomic sequences in PostScript

A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot:

 * Comprehensive alignment plots for any GFF-feature. Attributes are defined
   separately so you can modify only whatsoever attributes for a given file or
   share same customization across different data-sets.
 * All parameters are set by default within the program, but it can be also
   fully configured via gff2ps-like flexible customization files. Program can
   handle several of such files, summarizing all the settings before producing
   the corresponding figure. Moreover, all customization parameters can be set
   via command-line switches, which allows users to play with those parameters
   before adding any to a customization file.
 * Source order is taken from input files, if you swap file order you can
   visualize alignment and its annotation with the new input arrangement.
 * All alignment scores can be visualized in a PiP box below gff2aplot area,
   using grey-color scale, user-defined color scale or score-dependent
   gradients.
 * Scalable fonts, which can also be chosen among the basic PostScript default
   fonts. Feature and group labels can be rotated to improve readability in
   both annotation axes.
 * The program is still defined as a Unix filter so it can handle data from
   files, redirections and pipes, writing output to standard-output and
   warnings to standard error.
 * gff2aplot is able to manage many physical page formats (from A0 to A10, and
   more -see available page sizes in its manual-), including user-defined ones.
   This allows, for instance, the generation of poster size genomic maps, or
   the use of a continuous-paper supporting plotting device, either in portrait
   or landscape.
 * You can draw different alignments on same alignment plot and distinguish
   them by using different colors for each.
 * Shape dictionary has been expanded, so that further feature shapes are now
   available (see manual).
 * Annotation projections through alignment plots (so called ribbons) emulate
   transparencies via complementary color fill patterns. This feature allows
   to show color pseudo-blending when horizontal and vertical ribbons overlap.

Tags: Field: Biology, Bioinformatics, Implemented in: C, Perl, User Interface: Command Line, Command Shell, Role: Program, Scope: Utility, Purpose: Data Conversion, Data Visualization, Works with: Vector Image, Supports Format: Plain Text, PostScript

Other Packages Related to gff2aplot

• dep: libc0.1 (>= 2.7) [kfreebsd-amd64, kfreebsd-i386]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc0.1-udeb

• dep: libc0.3 (>= 2.11) [hurd-i386]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc0.3-udeb

• dep: libc6 (>= 2.11) [powerpcspe, sh4]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.13) [s390x]

  dep: libc6 (>= 2.5) [avr32]

  dep: libc6 (>= 2.5-5) [m68k]

  dep: libc6 (>= 2.7) [not alpha, avr32, hurd-i386, ia64, kfreebsd-amd64, kfreebsd-i386, m68k, powerpcspe, s390x, sh4]

• dep: libc6.1 (>= 2.7) [alpha, ia64]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• sug: gff2ps

  produces PostScript graphical output from GFF-files

• sug: postscript-viewer

  virtual package provided by evince, evince-gtk, ghostscript, gv, kghostview, okular

Download gff2aplot

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha	2.0-6	322.6 kB	788.0 kB	[list of files]
amd64	2.0-6	319.2 kB	784.0 kB	[list of files]
armel	2.0-6	325.5 kB	788.0 kB	[list of files]
armhf	2.0-6	322.3 kB	636.0 kB	[list of files]
avr32 (unofficial port)	2.0-5	320.7 kB	780.0 kB	[list of files]
hppa	2.0-6	322.0 kB	784.0 kB	[list of files]
hurd-i386	2.0-6	319.8 kB	776.0 kB	[list of files]
i386	2.0-6	318.7 kB	776.0 kB	[list of files]
ia64	2.0-6	324.4 kB	828.0 kB	[list of files]
kfreebsd-amd64	2.0-6	320.5 kB	698.0 kB	[list of files]
kfreebsd-i386	2.0-6	319.7 kB	692.0 kB	[list of files]
m68k (unofficial port)	2.0-5	319.1 kB	780.0 kB	[list of files]
mips	2.0-6	321.0 kB	792.0 kB	[list of files]
mipsel	2.0-6	319.5 kB	792.0 kB	[list of files]
powerpc	2.0-6	319.3 kB	780.0 kB	[list of files]
powerpcspe (unofficial port)	2.0-6	320.1 kB	780.0 kB	[list of files]
s390	2.0-6	321.0 kB	784.0 kB	[list of files]
s390x	2.0-6	323.7 kB	641.0 kB	[list of files]
sh4 (unofficial port)	2.0-6	325.9 kB	784.0 kB	[list of files]
sparc	2.0-6	319.4 kB	788.0 kB	[list of files]
sparc64 (unofficial port)	2.0-6	318.7 kB	792.0 kB	[list of files]