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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If you get error messages with this saying something about an out-of-date library,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"

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