SeqPup, version 0.9, September 1999

SeqPup is a biological sequence editor and analysis program.  It
includes links to network services and external analysis
programs.  It is usable on common computer systems that support
the Java runtime environment, including Macintosh, MS-Windows and
X-Windows.

This release is much easier to install and use.

Features include
  multiple sequence alignment and single sequence editing
  read and write several sequence file formats 
  sequence feature editing, manipulation and marking in prints
  translate dna/protein, consensus, reverse/complement, and distance methods 
  pretty print of alignments and sequences with boxed and shaded regions
  Internet Sequence Retrieval System (SRS), and NCBI-BLAST searches 
  User Plug-in sequence manipulations and analyses
  User-definable links to external analysis programs, including
    ClustalW multiple alignment, CAP contig assembly, tacg restriction map
  Remote program client-server interface, using CORBA protocol 

Additions to this Java release include sequence document and
feature manipulation and display, enhanced sequence file
handling, enhanced drawing/pretty print methods, including PDF
output, user-developed plug-in methods for sequence analysis and
display (Java classes),  improved single-sequence editing,
improved alignment manipulations.

This application is a work in progress; it has bugs still.  
Your comments are welcome.

Find this software at
  ftp://iubio.bio.indiana.edu/molbio/seqpup/java/ 
  http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/

Developers will find the source code for this application and others 
in the iubio:/molbio/java/source folder, in the dclap-src.zip file.  

Comments, bug reports and suggestions can be e-mailed to 
seqpup@bio.indiana.edu.


=== Usage and installation =====

You will need to fetch the SeqPup.jar java archive.  It includes
help documentation and data files, which will be installed when you
first run the program. 

To start SeqPup from MSWindows or Unix, use one of these command lines
  jre  -cp SeqPup.jar  run   (for Java 1.1.x with jre)
  java -cp SeqPup.jar  run   (for Java 1.2.x - not a recommended version)
  java -classpath SeqPup.jar:$CLASSPATH  run   (for Java 1.1.x without jre)
  
To start SeqPup from MacOS, use the MRJ application, in SeqPup9-macos.hqx.
Apple Java (MRJ) version 2.1.2 or later is recommended.
  
There are several external analysis applications available for SeqPup,
as compiled programs for MacOS and MSWindows.  Find these in
  seqpup9-methods-msdos.zip   (MS Windows ZIP archive)
  seqpup9-methods-macos.sit   (MacOS Stuffit archive)
These should be installed in a methods/ folder in the same folder as
SeqPup.jar.

Java version: This program will not work properly with the
Java 1.2 runtime that is now commonly available on MSWindows systems.
SeqPup will work with the Java 1.1.8 for MSWindows, which
can be installed in addition to Java 1.2.
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