Draw pretty views of biosequences, Java command-line version,
     to output in various graphic formats.
  drawseq example 

  Usage: jre -cp drawseq.jar run [options] input-file(s)

    styles=seqstyle.properties  use file with style properties instead of defaults
    colors=seqcolor.properties  use file with base color properties instead of defaults

    format=name         Format name for output
          see Formats   list below for names

    out[put]=out.pict   output file name
    in[put]=input.seq   input file name ('in=' not required)

    nativeawt           use native AWT toolkit (not good for Unix commandline use)
    pipe                Pipe (command line, stdout)
    verb[ose]           Verbose progress
    inform[at]=#        input sequence format number,  or
    inform[at]=Name     input sequence format name.  Assume input data is this format

    range=10..100       select sequences subrange
    feat[ures]=exon,CDS...   extract sequence of selected features
    nofeat[ures]=repeat_region,intron... remove sequence of selected features 
          Can't mix feature and nofeature. 
          Applies only with input feature tables.

   Styles values include (see example styles file for more)
    Sequence.width=50          sequence line width
    Sequence.nameleft=false    name on left/right side
    Sequence.numleft=true      seq index on left/right side
    Sequence.numtop=true       index on top/bottom

This program requires a Java runtime (jre) program, version 1.1.x 
All non-options (no '=') are used as input file names.

Drawseq version 1.0 (7++ September 1999)

Home of this package is http://iubio.bio.indiana.edu/soft/molbio/java/apps/drawseq/

An instance of the Web form for this is http://iubio.bio.indiana.edu/cgi-bin/drawseq.cgi

Available graphic output formats:
Available biosequence input formats:
 ID  Name             Read  Document  
  1  IG|Stanford      yes        --   
  2  GenBank|GB       yes       yes   
  3  NBRF             yes        --   
  4  EMBL             yes       yes   
  5  GCG              yes        --   
  6  DNAStrider       yes        --   
  8  Pearson|Fasta    yes        --   
 11  Phylip3.2        yes        --   
 12  Phylip|Phylip4   yes        --   
 13  Plain|Raw        yes        --   
 14  PIR|CODATA       yes        --   
 15  MSF              yes        --   
 17  PAUP|NEXUS       yes        --   
 19  BLAST            yes        --   
 20  XML              yes       yes   

Also available in this package:

For the current help document, use
jre -cp drawseq.jar help

  Graphic interface to Drawseq (Java swing)
    java -cp drawseq.jar iubio.drawseq.app (java version 1.2)
    jre -cp drawseq.jar:/path/to/swingall.jar iubio.drawseq.app (java version 1.1.x)
  Drawseq version 1.0 (7++ September 1999)

  Java Foundation Classes (Swing) are required for this interface
  This is available for Java versions 1.1.7 and newer at
  Put the swingall.jar of this package in your classpath, as with
    jre -cp drawseq.jar:swingall.jar iubio.drawseq.app (java version 1.1.x)

  Macintosh users: See also Drawseq.macapp, a small Mac Java application
  to launch drawseq.jar without a jre commandline.

HTTP server common gateway interface to Drawseq Usage (example as cgi on unix system): Install shell script like this as '/cgi-bin/drawseq.cgi' for your web server #!/bin/sh envtemp=/tmp/rseq$$.env env > ${envtemp} /usr/java/bin/jre -cp drawseq.jar iubio.drawseq.cgi env=${envtemp} /bin/rm ${envtemp} Drawseq version 1.0 (7++ September 1999) See also iubio.drawseq.run.usage()