Package: gff2aplot (2.0-13)

[ 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
   one to show color pseudo-blending when horizontal and vertical ribbons
   overlap.

Tags: Software Development: Perl Development, Libraries, Field: field::biology, field::biology:bioinformatics, Implemented in: C, implemented-in::perl, interface::commandline, User Interface: Command Shell, Role: role::devel-lib, role::program, Scope: Utility, Purpose: Data Conversion, use::viewing, works-with-format::plaintext, Supports Format: works-with-format::postscript, works-with::TODO, Works with: Image, works-with::image:vector, works-with::text

Other Packages Related to gff2aplot

• dep: libc6 (>= 2.17) [arm64, ppc64el]

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

  dep: libc6 (>= 2.7) [not arm64, ppc64el]

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• rec: ghostscript

  interpreter for the PostScript language and for PDF

• rec: graphicsmagick

  collection of image processing tools

  or imagemagick

  image manipulation programs -- binaries
  also a virtual package provided by graphicsmagick-imagemagick-compat, imagemagick-6.q16

• sug: gff2ps

  produces PostScript graphical output from GFF-files

• sug: postscript-viewer

  virtual package provided by atril, evince, ghostscript, gv, okular, qpdfview-ps-plugin, zathura-ps

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amd64	240.4 kB	1,451.0 kB	[list of files]
arm64	238.1 kB	1,443.0 kB	[list of files]
armel	241.7 kB	1,451.0 kB	[list of files]
armhf	240.3 kB	1,439.0 kB	[list of files]
i386	239.6 kB	1,451.0 kB	[list of files]
mips64el	238.5 kB	1,457.0 kB	[list of files]
mipsel	239.3 kB	1,448.0 kB	[list of files]
ppc64el	239.6 kB	1,484.0 kB	[list of files]
s390x	238.6 kB	1,447.0 kB	[list of files]