IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

various questions in the Mac environment

Jim Woodgett jwoodget at ocicl.oci.utoronto.ca
Mon Dec 6 13:53:22 EST 1993


In article <scott.755199530 at phylo>, scott at phylo.life.uiuc.edu (Scott Howard) 
writes:
 
> Shaded Annotated Sequences: 
> GeneWorks and DNAStar will accomplish this. If you'd like to save 
> yourself a few thousand francs, 13 point Courier and most any 
> reasonably well constructed drawing program will suffice. 

There is a non-commercial possibility if you are using a Macintosh - SeqApp 
1.9.  This does a very nice multicoloured pretty print with shading as well 
as lots of other things.  It was written by Don Gilbert and is free (as far 
as I know).  Note it is an alpha release and may cause crashes.  I have 
experienced these but usually they simply cause the program to quit.   It's a 
really nice piece of work overall.  Here is Don's abstract on the program:
 
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 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 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. 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. 


Jim Woodgett      Fax (416) 926 6529     Tel (416) 924 0671
jwoodget at ocicl.oci.utoronto.ca
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