aligned sequences editing software

Hans Sluiman h.sluiman at rbge.org.uk
Thu Feb 4 07:35:40 EST 1999


Diederik van Tuinen wrote:
> 
> I am looking for a software, hopefully shareware and runing on MacOS,
> allowing to edit aligned sequences - adding or removing gaps - after a
> clustalv run.
> 
> --
> Dr. D. van Tuinen
> INRA
> Laboratoire de Phytoparasitologie INRA/CNRS
> Centre de Microbiologie du Sol et de l'Environnement
> Domaine d'Epoisses
> 21110  BRETENIERES

SeqPup, version 0.7, August 1997

see the folder iubio:/molbio/seqpup/java/ for this new version
see the folder iubio:/molbio/seqpup/c++/ for the older, but currently
more complete version

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, including Macintosh, MS-Windows and X-Windows.  

Features include
        multiple sequence alignment and single sequence editing
        ! read and write several sequence file formats 
        *! sequence feature editing, and marking in prints
        translate dna/amino, consensus, reverse/complement, distance and
such functions 
        pretty print of alignments and sequences with boxed and shaded regions
        Internet sequence analysis:
          * fetch sequeces using SRS keyword search
          * NCBI-BLAST similarity search
    (this version: * - new; ! - incomplete)

NOTICE: This application is a work in progress; it has bugs. It may be useful
to you as is, but it is still prone to problems.

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

SeqPup is being written using DCLAP, a free and portable class application
framework, now converted to the new Java language. This Java version
will work 
on any computer system that supports Java runtime version 1.0.2,
including Macintosh, 
MS Windows, and many Unix systems. 

Java versions of other molecular biology applications of mine will
soon be updated (maybe by 26 Aug 97):
   loopDloop - an RNA secondary structure display editor
   Phylodendron - a phylogenetic tree drawing application
   FlyNapp - a FlyBase database network application

Developers will find the source code for this application and others in the
iubio:/molbio/java/source folders.




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