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gff2aplot

pair-wise alignment-plots for genomic sequences in PostScript

/Main/Debian/amd64/science/

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

Info:

Homepage:	-
Package version:	2.0-3
Architecture:	amd64
Distribution:	Debian
Filename:	gff2aplot_2.0-3_amd64.deb

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2005-03-19  ftp://ftp.linux.it/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.cesca.es/mirror/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.uni-frankfurt.de/pub/Mirrors3/debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.uni-magdeburg.de/pub/mirror/linux/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://debian.lcs.mit.edu/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.kfki.hu/pub/linux/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.skynet.be/mirror1/debian.org/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.prz.rzeszow.pl/pub/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.3logic.net/.1/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.uic.nnov.ru/pub/Linux/Debian/debian-amd64/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.wustl.edu/pub/linux/distributions/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.nz.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.uni-hannover.de/pub/mirror/linux/debian-mirror/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.port80.se/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
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2005-03-19  ftp://ftp.wh2.tu-dresden.de/pub/mirrors/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.mgts.by/pub/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.uni-kassel.de/Mirrors1/ftp.de.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
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2005-03-19  ftp://ftp.rfc822.org/pub/mirror/ftp.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.fr.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.lf.net/pub/Mirrors/ftp.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
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2005-03-19  ftp://64.15.134.18/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.ps.pl/dsk0/ftp.debian.org/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.free.fr/.mirrors1/ftp.debian.org/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp13.freebsd.org/pub/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.ankara.edu.tr/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.uni-oldenburg.de/linux/ftp.debian.org/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.fi.debian.org/pub/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.nl.kernel.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-18  ftp://ftp.zcu.cz/pub/linux/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.auckland.ac.nz/linux/dists/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.tu-ilmenau.de/Mirrors/ftp.de.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.cvut.cz/mirrors/debian.org/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.csie.chu.edu.tw/pub2/Debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://161.53.160.16/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.carnet.hr/misc/.ftp.hr.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2006-03-18  ftp://ftp.uni-stuttgart.de/pub/mirror/ftp.de.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://193.219.61.67/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.uwa.edu.au/mirrors/linux/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.botik.ru/pub/linux/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.univ-savoie.fr/pub1/ftp.fr.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.med.univ-tours.fr/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.psn.ru/pub/Linux/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb
2005-03-19  ftp://ftp.linux.pt/pub/mirrors/debian/pool/main/g/gff2aplot/gff2aplot_2.0-3_amd64.deb