SeqApp, Mac sequence editor, is updated

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Mon Oct 5 16:26:18 EST 1992

SeqApp, version 1.8a, is a semi-major update of this Macintosh
biosequence editor, analyzer, and network handyman.

The various enhancements and corrections include 
- major changes to the sequence print-out options, 
   including addition of a dotplot display (courtesy of DottyPlot), 
   a phylogeny tree display (courtesy of TreeDraw Deck & J. Felsenstein's 
   much enhanced Pretty Print for single and aligned sequences
- addition and updating of several e-mail service links, 
   including Blast Search and Genbank Fetch via NCBI,
   BLOCKS, Genmark, and Pythia services,
- updated Internet gopher client (equal to GopherApp),
- editable Child Tasks dialogs
- addition of links to Phylip applications as Child Tasks
- addition of Phylip interleaved format as sequence output option

More general background:

SeqApp is a biological sequence editor and analysis program for
Macintosh computers.  It includes links to network services and 
external analysis programs.

Features include	
	multiple sequence alignment editor
	single sequence editor window
	read and write several sequence file formats
	easy hand alignment features including colored bases and sliding
	automatic multiple sequence alignment thru Clustal external app 
	automatic gel fragment alignment to contigs thru exernal app
	consensus,reverse,complement,degap operations
	restriction maps
	dot plots
	translate dna to/from protein using various codon tables
	automatic preference saving
	internet send mail, read mail
	internet gopher, information retreival including genbank.
	internet sequence analysis services
	user-definable links to external analysis programs
	and more

*** NOTICE:  This is an early, unfinished version of the
program.   Expect it to fail in various ways.  This release is
made available to those who wish to test and comment on its
future development. 

SeqApp is being written by Don Gilbert, using the MacApp 
extensible Macintosh programming framework from Apple Computer.

You can obtain updates of this release thru anonymous ftp to 
ftp.bio.indiana.edu, in folder /molbio/seqapp, as seqapp.hqx. 
You may also obtain updates directly thru an internet-connected
Mac with SeqApp, using Gopher to the IUBio archive.  Look for a
folder called "IUBio Software+Data/SeqApp, Mac sequence editor".

There are two other distribution files with accessory programs
for SeqApp.  One is "child-apps.hqx", which contains the
programs ClustalV, BBEdit, FragAlign and possibly other applications
called by SeqApp.   The other is "fragalign-src.hqx" which contains
the source code to FragAlign, showing how a command-line program
can be modified for use with SeqApp.

This release of SeqApp should work on all Mac models from
the Mac SE and Mac II to newer ones.   It should work properly
under Mac systems 6 and 7, though it has some features only for
sys 7.

Comments, bug reports and suggestions for new features (see
below) may be addressed via e-mail to

   SeqApp at Bio.Indiana.Edu

Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405

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