gff2aplot

About gff2aplot

From Debian's package description

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.

From Debian's description of the gff2aplot package, under that package's license.