SeqApp, Mac sequence editor, is updated

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Sat Jun 12 17:28:05 EST 1993


SeqApp is a Macintosh biosequence editor, analyzer, and network 
handyman.  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 CAP 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
	
* These features were updated in release 1.9a.  See below for details.

NOTICE:  This program is not finished, and may fail in various ways.  Please 
send notice of any problems you have using it to the address below. This 
release will expire on a date indicated in the About dialog. 

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 may be additional distribution software, 
data or information in this /molbio/seqapp folder.  See the Readme files in 
it for details. 

As of release 1.9a157, SeqApp fails once again to work on a Mac SE, or on any 
Mac running system software earlier than 7.0.  

Comments, bug reports and suggestions for new features may be sent by e-mail to

	     SeqApp at Bio.Indiana.Edu


History

SeqApp was started Sept. 1990 as MacApp sequence editor/analysis platform  on 
which analysis programs from other authors, typically command line w/ weak user 
interfaces, could be easily incorporated into a useable Mac interface.

12 June 93, version 1.9a159 -- a semi-major update, and time extension  
with various enhancements and corrections.  These include
  -- lock/unlock indels (alignment gaps). Useful when sliding bases around
     during hand alignment, to keep alignment fixed in some sections.
  -- color amino (and nucleic) acids of your choice.  
  -- added support for more sequence file formats: MSF, PAUP, PIR.  SeqApp now 
     relies on the current Readseq code for sequence reading & writing.
  -- save selection option to save subset of bases to file.
  -- addition the useful contig assembly program CAP, written by Xiaoqiu Huang.
  -- major revision of preference saving method (less buggy, I hope)
  -- major revision of the underlying application framework, due to moving from 
     MacApp 2 to MacApp 3.
  -- fixed a bug that caused loss of data when alignment with a selection was 
     saved to disk.



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




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