Step 8: Downloads
Everything we've used so far has been freeware on the Web. For the last page of the tutorial, I'll share with you three pieces of downloadable freeware that I use on a regular basis.
ClustalW 1.83 XP
This is the downloadable version of ClustalW I referred to previously. It has somewhat more functionality than the Web version, as you can use it to produce bootstrapped Phylip-format trees (.phb files). There are three important tips to using it, though. One, you must download 1.83 XP if you use Windows XP or it won't work. Two, you have to run it from the directory your alignment files are in. Three, the downloadable client uses the old DOS file name conventions, so you have to have filenames of eight letter or less, like "12345678.txt". It's faster and easier once you do get used to it, though.
BioEdit
This is the sequence alignment editor I generally use instead of JalView. I open my .aln files in BioEdit to look for good primer locations and what have you. It's easier and more functional than JalView, plus it's easier to read.
TreeView
This is the software I usually use to view and play with trees. JalView's tree editor has a couple of flaws in it I don't like, or at least user errors. I haven't figured out how to set a scale bar and I haven't figured out how to set a root organism. These are both important to making attractive trees, and they're both easily done in TreeView. TreeView can read Phylip format or ClustalW format trees.