NCBI

Starting with the Prokaryotic Genome Project homepage...

FOR TWO ORGANISMS

1. Scroll down to find the genome of interest.
2. Click the NC_ accession link from the RefSeq column.
3. Click GenePlot (if available) from the BLAST homologs column of the resulting table interface.
4. Select the two organisms of choice and then click "Compare Selected Pair".

FOR THREE ORGANISMS

1. Proceed as in Steps 1 and 2 above.
2. Select TaxPlot from the BLAST homologs column of the resulting table interface.
3. Select two other organisms from the drop-down menus below the selected genome of interest.
4. Click the "compare" button located just below the graphical plot.