Pakket: gff2aplot (2.0-15)

[ Bron: 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: Softwareontwikkeling: Ontwikkelen in Perl, Bibliotheken, 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

Andere aan gff2aplot gerelateerde pakketten

• dep: libc6 (>= 2.34) [niet alpha, ia64, sh4]

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  Ook een virtueel pakket geboden door: libc6-udeb

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• dep: libc6.1 (>= 2.34) [alpha]

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  Ook een virtueel pakket geboden door: libc6.1-udeb

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• dep: perl

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• rec: ghostscript

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• sug: gff2ps

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• sug: postscript-viewer

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gff2aplot downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Pakketgrootte	Geïnstalleerde grootte	Bestanden
alpha (unofficial port)	237,4 kB	1.483,0 kB	[overzicht]
amd64	238,4 kB	1.447,0 kB	[overzicht]
arm64	236,8 kB	1.482,0 kB	[overzicht]
armel	240,5 kB	1.450,0 kB	[overzicht]
armhf	238,4 kB	1.438,0 kB	[overzicht]
hppa (unofficial port)	238,4 kB	1.442,0 kB	[overzicht]
i386	238,9 kB	1.450,0 kB	[overzicht]
ia64 (unofficial port)	241,7 kB	1.462,0 kB	[overzicht]
m68k (unofficial port)	236,3 kB	1.442,0 kB	[overzicht]
mips64el	237,5 kB	1.483,0 kB	[overzicht]
ppc64 (unofficial port)	238,8 kB	1.483,0 kB	[overzicht]
ppc64el	239,2 kB	1.483,0 kB	[overzicht]
riscv64	238,8 kB	1.442,0 kB	[overzicht]
s390x	238,7 kB	1.446,0 kB	[overzicht]
sh4 (unofficial port)	240,1 kB	1.482,0 kB	[overzicht]
sparc64 (unofficial port)	239,1 kB	2.443,0 kB	[overzicht]
x32 (unofficial port)	238,6 kB	1.446,0 kB	[overzicht]