You must read TermsOfUsage before installing or using any of this software.

You should obtain the user's guide from the CDSplotcon webpage, for more 
  information.



INSTALLATION:

First unzip and unpack the distribution file:

gunzip CDSplotcon.tar.gz 
tar xvf CDSplotcon.tar 
cd CDSplotcon

This will give you the files:

aa2codon.dat  EXAMPLE1/   mlrgd.R         README           runmean.cxx
aa.dat        EXAMPLE2/   ntadjust.cxx    redo_mlrgd       run_mlrgd
addgaps.cxx   minmax.cxx  ntunadjust.cxx  redo_plots       TermsOfUsage
codon.dat     mlrgd.cxx   nuc.dat         runclipmean.cxx

Now compile the programmes (replace 'g++' by an appropriate alternative, 
  e.g. 'c++' or 'gcc', if you're using a different C++ compiler):

g++ -o addgaps addgaps.cxx 
g++ -o minmax minmax.cxx
g++ -o mlrgd mlrgd.cxx
g++ -o ntadjust ntadjust.cxx
g++ -o runclipmean runclipmean.cxx
g++ -o runmean runmean.cxx

Then copy these programmes to your ~/bin directory:

mkdir ~/bin
cp addgaps     ~/bin
cp minmax      ~/bin
cp mlrgd       ~/bin
cp ntadjust    ~/bin
cp runclipmean ~/bin
cp runmean     ~/bin

Also make sure that run_mlrgd, redo_mlrgd and redo_plots are executable:

chmod u+x run_mlrgd redo_mlrgd redo_plots



REQUIRED SOFTWARE:

You will also need to download and install the following software if you don't 
already have it:

code2aln     Sequence alignment programme.
             Obtain from http://www.tbi.univie.ac.at/~roman/Code2aln/

seqret       Part of the EMBOSS package.
seqretsplit  Obtain from http://emboss.sourceforge.net/
infoseq 
degapseq 
               
ednaml       Phylogeny programmes in the PHYLIP package.
ednapars     Repackaged as part of the EMBASSY package.  
             Obtain from http://emboss.sourceforge.net/

R            Statistics and graphics package.
             Obtain from http://www.r-project.org/



RUNNING CDSplotcon:

Use the script run_mlrgd.  Open run_mlrgd in a text-editor and edit the 
parameters in the 'Options' section if you like.  Make sure run_mlrgd, 
aa2codon.dat, aa.dat, codon.dat and nuc.dat (and redo_mlrgd, redo_plots, 
if required) are in the working directory, together with the input sequences,
sequence list and ORF annotation.  Then type

./run_mlrgd 'prefix'

where 'prefix'.seqs is the name of the sequences list.



EXAMPLES:

1) Hepatitis B Virus example.

cd EXAMPLE1
./run_mlrgd hbv

Note that a few of the parameters in EXAMPLE1/run_mlrgd differ from those in 
the default run_mlrgd - e.g. the 'circular' genome option is switched on. 

The output file 'hbv.fcm.eps' (view with e.g. 'ggv hbv.fcm.eps', or use
'epstopdf hbv.fcm.eps' then 'xpdf hbv.fcm.pdf') contains the conservation 
plots for the full-coding model.  See the user's guide for details of all the 
other output files.

2) Barley Yellow Dwarf Virus example.

cd EXAMPLE2
./run_mlrgd bydv




Note for MacOS-X users:

I've noticed that MacOS-X tends to have a system-wide maximum
stacksize limit of 65536 kB.  To avoid exceeding this limit (resulting
in a 'Segmentation Fault' error), you may need to edit the lines

#define maxlength 50000
#define maxpairs 200

to 

#define maxlength 10000
#define maxpairs 20

in mlrgd.cxx before compiling.  Unfortunately this will limit the
maximum length of input sequences to 10000 nt and maximum number of
input sequences to 10.