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?)