SeqPup, version 0.5 development release, January 1996 Abstract SeqPup is a biological sequence editor and analysis program usable on the common computer systems including Macintosh, MS-Windows and X-Windows. It includes links to network services and external analysis programs. Features include multiple sequence alignment editor single sequence editor read and write several sequence file formats easy hand alignment features including colored bases and sliding automatic multiple sequence alignment with ClustalW app automatic gel fragment alignment to contigs with CAP app phylogenetic analysis of alignments with fastDNAml and LSADT apps phylogenetic tree drawing with DrawTree and DrawGram Phylip apps consensus, reverse, complement, degap, and distance/similarity operations restriction maps pretty print of alignments and sequences with boxed and shaded regions. translate dna to/from protein using various codon tables find strings and ORFs automatic preference saving internet send mail and sequence analysis services by email user-definable links to external analysis programs NOTICE: This release is still unfinish, and has bugs. Please careful of trusting important work to it. Yet it may be useful to some of you as is. SeqPup is being written by Don Gilbert using DCLAP, a free, portable C++ class application framework, and founded on the NCBI Toolkit, especially it's Vibrant user-interface section written primarily by Jonathan Kans. SeqApp/SeqPup was started in 1990 as sequence editor/analysis platform on which analysis programs from other authors could be easily incorporated into a useable interface. It was originally written with Apple Computer's MacApp application framework. You can obtain this release thru anonymous ftp, gopher or http to iubio.bio.indiana.edu, in folder /molbio/seqpup. Versions are available for Macintosh, MS Windows, and various Unix/XWindows systems. The Internet locators to this software are Source code for this software is at . Comments, bug reports and suggestions for new features (see below) are very welcome and should be sent via e-mail to . Jan 96 - version 0.5b: added configurable child-app parameters as HTML forms; fixed file path handling; added LSADT, DrawTree and DrawGram child apps; fixed save-file-in- place; better data table and child app handling; added seq mask items ; click-top-index-line to select columns; fix for GCG-MSF format ('-' to '.' translate); several MS- Win32/NT/95 updates; Mac file bundle rez & finder-open; added seq-index display; added variable position grey coloring; added mswin/xwin sticky menubar; fixed mswin mouse- shift commands;added mswin menu command keys; fixed mac/mswin text edit command keys; save pretty print in PICT format (mac), metafile (mswin - still buggy?)