Apologies if this has already been answered, but if I want to update samtools 1.3 to the latest release, what's the best way to go about it? Uninstall the older version first and then do a fresh install, or is there a update command that automatically does that from the terminal? 
Remove the old version and install the new one (or just install the new one over top). But really, as Wouter mentioned, conda is your friend: `conda install -c bioconda samtools`. I recommend making a separate conda environment for each software version, since then you don't have to worry something breaking because you've accidentally up/down-graded some random dependency of another tool.