SeqPup biosequence editor version 0.5 release

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Fri Jan 19 18:43:43 EST 1996


SeqPup, version 0.5 development release, January 1996

This update includes better handling for external (child)
applications, including user-configurable HTML forms dialogs, 
better support for new MSWindows systems (95,NT,32s),
added apps of fastDNAml 1.1.1, LSADT, Drawtree/Drawgram,
various corrections, addeed alignment display and handling features,
and others (see documents).

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

Features include
     * multiple sequence alignment editor
     single sequence editor
     read and write several sequence file formats
     * easy hand alignment features including colored bases and sliding
     automatic multiple sequence alignment with ClustalW app
     automatic gel fragment alignment to contigs with CAP app
     * phylogenetic analysis of alignments with fastDNAml and LSADT apps
     * phylogenetic tree drawing with DrawTree and DrawGram Phylip apps
     consensus, reverse, complement, degap, and * distance/similarity operations
     restriction maps
     * pretty print of alignments and sequences with boxed and shaded regions.
     translate dna to/from protein using various codon tables
     find strings and ORFs
     automatic preference saving
     internet send mail and sequence analysis services by email
     user-definable links to external analysis programs

* new or updated in this release

NOTICE:  This release is still unfinish, and has bugs.
Please careful of trusting important work to it.  Yet it may
be useful to some of you as is.

You can obtain this release thru anonymous ftp, gopher or
http to iubio.bio.indiana.edu, in folder /molbio/seqpup.
Versions are available for Macintosh, MS Windows, and
various Unix/XWindows systems.   The Internet locators to
this software are

  <ftp://iubio.bio.indiana.edu/molbio/seqpup/>
  <gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/seqpup/>
  <http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/>

Source code for this software is at
  <ftp://iubio.bio.indiana.edu/util/dclap/source/>.
Comments, bug reports and suggestions for new features (see
below) are very welcome and should be sent via e-mail to
<mailto://SeqPup@Bio.Indiana.Edu/>.

Please note that the following versions have not been updated yet 
due to time constraints and that they are not as well supported
by my development software:
   MSWindows 3/16-bit
   SunOS4-Sparc

The following versions are updated to 0.5
   Mac (PPC and 68k)
   MSWin 32bit (95,NT,32s)
   DEC-Alpha-OSF
   SGI-Irix5
   Sun-Solaris2

-- 
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu




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