Source: gff2aplot Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional Build-Depends: debhelper-compat (= 13) Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/gff2aplot Vcs-Git: https://salsa.debian.org/med-team/gff2aplot.git Homepage: https://genome.crg.es/software/gfftools/GFF2APLOT.html Rules-Requires-Root: no Package: gff2aplot Architecture: any Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends} Recommends: graphicsmagick | imagemagick, ghostscript Suggests: postscript-viewer, gff2ps Description: 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.