NOTE: This is an OLD version of seqapp. See the newer version in seqapp.hqx file, and use this only if the newer version fails for you. Please also report such failure to the address below. This old version will not be updated and will expire soon. 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. 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 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 now 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. If you obtain this release thru FTP file transfer, you have a binhex encoded archive file. You will need the Stuffit or Unstuffit applications. The former includes an un-binhex (decode?) option to convert from text encoding to macbinary Stuffit archive. These are widely available from Mac software archives, user groups, and computing support people. Use Stuffit to extract the SeqApp distribution folder. The file SeqApp.Help is a plain text file which may be read from your favorite wordprocessor or from the Edit program in the Apps folder. If you have problems getting SeqApp to launch, and cannot read this help from SeqApp, please read it with another application to help solve the problem. Comments, bug reports and suggestions for new features (see below) may be addressed via e-mail to SeqApp@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. 20 Jun 93, version 1.8a156 -- same as 1.8a154, except expiration date is moved to July 1994. Version 1.9 is now available but currently fails to work in a few cases where 1.8 will work (system 6, Mac SE). This version is an interim aid to those who need find version 1.9 fails for them. 12 Nov 92, version 1.8a154 -- interim bug fix release. Cures problem introduced in version 1.8a153: sequence data was lost when the "sliding bases" feature of adding gaps was used, then the document was saved. 5 Oct 92, version 1.8a153 -- a semi-major update with various enhancements and corrections. These include - corrections to the main alignment display, - improvements to the help system, - major changes to the sequence print-out options, -- including addition of a dotplot display (curtesy of DottyPlot), -- a phylogeny tree display (courtesy of TreeDraw Deck & J. Felsenstein's DrawTree), -- improved Pretty Print, which now has a single sequence form and a better aligned sequence form, -- improved Restriction map display, - 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