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gff2aplot

pair-wise alignment-plots for genomic sequences in PostScript

Variants:
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:
Package version:2.0-7
Architecture:s390
Distribution:Debian
Filename:gff2aplot_2.0-7_s390.deb

/usr/share/doc/gff2aplot/README.gz

##
## README FOR GFF2APLOT v2.0
##
##
## $Id: README,v 1.1 2003/03/17 17:58:46 jabril Exp $
##

  Dear User:

    This file contains important program information. Please read
  these tips through carefully, before beginning to work with GFF2APLOT.
  See INSTALL file for further tips on how to install the program
  and related scripts on your system.


---------------------------------------------
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/usr/share/doc/gff2aplot/examples/mhcregion/README.gz

##################################################
#
# README mhcregion
#
# This README runs as a shell script.
# Here you can find the commands
# we used to produce all the figures for:
#
#   "Analysis of a Syntenic Region by SIM"
#
# USAGE: bash README > .log 2>&1
#
# $Id: README,v 1.1 2003/03/04 18:06:17 jabril Exp $
#
##################################################
#
SECONDS=0 ;
#

#
# Orig
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/usr/share/doc/gff2aplot/examples/splice_sites/README.gz

##################################################
#
# README splice_sites
#
# This README runs as a shell script.
# Here you can find the commands
# we used to produce all the figures for:
#
#   ""
#
# USAGE: bash README > .log 2>&1
#
# $Id: README,v 1.2 2003/03/04 19:06:09 jabril Exp $
#
##################################################
#
SECONDS=0 ;
#

#
# Original Files
#
# KCRB.AG.hs.gff KCR
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/usr/share/doc/gff2aplot/examples/wublast/README.gz

##################################################
#
# README wublast
#
# This README runs as a shel
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/usr/share/man/man1/ali2gff.1.gz

ALI2GFF(1)                                                ALI2GFF(1)



NAME
       ali2gff  - Modul
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/usr/share/man/man1/blat2gff.1.gz

BLAT2GFF(1)                                              BLAT2GFF(1)



NAME
       blat2gff - Conve
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/usr/share/man/man1/gff2aplot.1.gz

GFF2APLOT(1)                                            GFF2APLOT(1)



NAME
       gff2aplot  -  Co
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/usr/share/man/man1/parseblast.1.gz

PARSEBLAST(1)                                          PARSEBLAST(1)



NAME
       parseblast - Fil
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