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.
