Required software and files

run_mlrgd will die if any of the following software is missing.

mlrgd runmean runclipmean addgaps minmax ntadjust	C++ programmes in the CDS-plotcon package.
run_mlrgd mlrgd.R	Scripts in the CDS-plotcon package. These will need to be in the running directory.
aa2codon.dat aa.dat codon.dat nuc.dat	Amino acid, codon and nucleotide matrices. These will need to be in the running directory.
code2aln	Sequence alignment programme. Obtain from http://www.tbi.univie.ac.at/$\sim$roman/Code2aln/.
seqret seqretsplit infoseq degapseq	Part of the EMBOSS package. Obtain from http://emboss.sourceforge.net/.
ednaml ednapars	Phylogeny programmes in the PHYLIP package. 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/.