Package: gff2aplot (2.0-3)

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.

Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html

Tags: Field: Biology, Implemented in: Perl, User Interface: Command Shell, Role: Program, Scope: Utility, Purpose: Data Conversion, Works with: Text, Supports Format: PostScript