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[ Source: gff2aplot  ]

Package: gff2aplot (2.0-14 and others)

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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
 * 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

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

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Download gff2aplot

Download for all available architectures
Architecture Version Package Size Installed Size Files
alpha (unofficial port) 2.0-14 239.8 kB1,452.0 kB [list of files]
amd64 2.0-14 240.0 kB1,451.0 kB [list of files]
arm64 2.0-14 238.6 kB1,443.0 kB [list of files]
armel 2.0-14 241.5 kB1,451.0 kB [list of files]
armhf 2.0-14 239.4 kB1,439.0 kB [list of files]
hppa (unofficial port) 2.0-14 239.6 kB1,443.0 kB [list of files]
i386 2.0-14 239.8 kB1,451.0 kB [list of files]
ia64 (unofficial port) 2.0-14 243.6 kB1,463.0 kB [list of files]
m68k (unofficial port) 2.0-14 238.3 kB1,451.0 kB [list of files]
mips64el 2.0-14 238.9 kB1,457.0 kB [list of files]
mipsel 2.0-14+b2 238.8 kB1,485.0 kB [list of files]
ppc64 (unofficial port) 2.0-14 239.8 kB1,484.0 kB [list of files]
ppc64el 2.0-14 239.0 kB1,484.0 kB [list of files]
riscv64 (unofficial port) 2.0-14+b1 239.2 kB1,444.0 kB [list of files]
s390x 2.0-14 239.0 kB1,447.0 kB [list of files]
sh4 (unofficial port) 2.0-14 241.2 kB1,443.0 kB [list of files]
sparc64 (unofficial port) 2.0-14 239.3 kB1,452.0 kB [list of files]
x32 (unofficial port) 2.0-14 239.8 kB1,447.0 kB [list of files]