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Paketbeschreibung


Paketnamegff2aplot
Beschreibungpair-wise alignment-plots for genomic sequences in PostScript
Archiv/RepositoryOffizielles Ubuntu Archiv lucid (universe)
Version2.0-5
Sektionuniverse/science
Prioritätoptional
Installierte Größe780 Byte
Hängt ab vonlibc6 (>= 2.4), perl
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PaketbetreuerUbuntu MOTU Developers
Quelle
Paketgröße327172 Byte
Prüfsumme MD5894ade847d3b2ddbc482b71a5e97b9e1
Prüfsumme SHA149e5a6246ca8cfacbfadfcc34ed37614920351c4
Prüfsumme SHA256871fff86ff606aac53c9afb954c2f5a8f198faf765164bfb49287bd774abb723
Link zum Herunterladengff2aplot_2.0-5_i386.deb
Ausführliche BeschreibungA 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.


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