SeqPup is distributed over the Internet in archive files. The archive format used is commonly available on the computer system you use (HQX self-extracting for Macintosh, ZIP for MS Windows, and tar + Gnu ZIP for Unix). There is one primary program, several document and data files, examples, and child application programs.
The current organization of files used by the program is:
SeqPup -- execuable, called "seqpup.exe" in MSDOS
SeqPup.help -- this document, in Microsoft RTF format
SeqPup.prefs -- settings for the program, in text format.
tables/ -- data files, required for Restriction maps, translate and some other functions. These are standard bioinformatics data files available and updateable from various sources.
codon.table -- table of codon preferences, in GCG format
renzyme.table -- REBase data file, for restriction maps, in GCG format
color.table -- table of color values for display of bases
hum.cod, tob.cod, eco.cod, and other codon preference tables that can substitute for codon.table at your preference
apps/ -- a selection of external analysis applications.
clustalw -- multiple sequence alignment
cap2 -- contig alignment
fastDNAml -- phylogenetic analysis of sequences
lsadt -- De Soete Least Squares phylogeny analysis
drawtree -- draw unrooted tree, from Phylip
drawgram -- draw cladograms, from Phylip
Note for Sun systems: This program requires theMotif run-time libraries that are commonly found on other XWindow systems. Motif is not standard on SunOS and is not part of Solaris until verson 2.4. If you have Solaris 2.3 or earlier, or SunOS, and do not know that your system includes Motif, then you will need the version with statically bound Motif libraries (SeqPup-sunos-mostat.gz).
If you have Solaris 2.4, or a version where Motif libraries are present, you may still need to configure the system to let SeqPup know where they are. In a Solaris 2.4 system, where motif lives in /usr/dt/lib by default, this may be needed to run successfully:
setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":/usr/dt/lib
If you get error messages with this saying something about an out-of-date library,
try instead putting the Motif /dt/lib in front:
setenv LD_LIBRARY_PATH /usr/dt/lib:"$LD_LIBRARY_PATH"