Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_22 Running the Phylogeny Inference Package programs PHYLIP
        at MUSC.

1) The complete set of PHYLIP programs is available for your use. 
   The programs are available without special software. Any telnet
   session to any research workstation will give you access.Running
   the programs is a matter of preparing the input files and then
   typing the program name. However, what follows is specialized 
   for molecular sequence data rather that character analysis. 

2) PHYLIP does NOT create multiple sequence alignments but the 
   programs REQUIRE that you supply such an alignment.

3) PHYLIP formatted multiple sequence alignments may be produced
   most conveniently from appropriate selection of output
   parameters within the CLUSTALW program. In addition,
   programs such as PAUP and MACCLADE can read GCG MSF files 
   and output PHYLIP format. Typing "readseq" from the  MUSC
   UNIX command line, starts a file inter-conversion
   program which can read multiple formats and write multiple
   formats including PHYLIP.

4) Once you have your PHYLIP format multiple alignment, type the
   following command:
   
   cp my_mult_align.phylip infile

   This uses UNIX copy ("cp") to copy the contents to a file named
   infile. The name "infile" is the dummy name which most PHYLIP
   programs automatically look to for input. Keep track of what file
   you currently have copied to the infile!

5) At his point typing say "dnadist" will start the DNA DISTANCE
   program which will in turn read the contents of the current
   infile and open a UNIX menu interaction BOX where you are asked to supply
   pertenant information. When you have the run customized you type
   the letter "y" for yes and the program executes.

6) The results of the current run are written to another dummy file
   called "outfile". In some cases, results also go to a dummy file
   called "treefile" or even "outtree". These are all ASCII files
   and can be viewed immediately.

7) Its a good idea to copy the generic outfile, treefile etc to 
   specific informative file names. Remember that in UNIX white
   space is significant.
   
   cp outfile my_mult_align.dnadistout

8) The treefile output can be printed with the elegant drawgram and drawtree
   programs. In both cases, drawtree and drawgram will look in your local
   directory for a font file. They won't find it and will prompt you for 
   the font file location. When that happens type this:
   
   /usr/common/bcr/font1

   and the programs will proceed. Typically, I select Laserwriter and opt 
   not to view the results on-screen. Drawtree and Drawgram write to the
   generic file name called "plotfile". This ascii postscript file may be
   transferred to a PC for printing (eg CorellDraw or DROP PS) or viewing
   (GhostScript) or viewed on the SGI UNIX system with "xpsview".