Run time

The conservation programme mlrgd is very quick. On my LINUX PC with a 2.6 GHz Pentium$^{\mathrm R}$ 4 processor) it takes $\sim$20-40 s (depending on the parameter options) to run mlrgd on the Hepatitis B example alignment. Much more time-consuming is the initial alignment (with code2aln) and the phylogenetic tree calculation with dnaml (dnapars is much quicker and is recommended for alignments of more than about 15 sequences). The time requirements of code2aln and dnaml are very dependent on the number of sequences. The scripts redo_mlrgd and redo_plots allow one to rerun the conservation programme and redo the plots with different parameters without having to rerun code2aln and dnaml.