A path is the location of a file or directory. They can be absolute or relative. Most simply, imagine we have the following directory structure on the server:
root directory

If we are in subdirectory3, and want to specify file3, we would simply type file3. If we are in directory2, and want to specify file3, we would simply type subdirectory3/file3. If we were in the root directory, and want to specify file3, we would type directory2/subdirectory3/file3. If we were in subdirectory3, and wanted to specify file2, we would type ../file2 (../ means look in the directory containing the current directory; ../../ means move up two directories, etc.). These are all relative paths -- what we type depends on where we are. Absolute paths start at the root directory and so start with /. No matter where we are, for example, /directory2/subdirectory3/file3 specifies file3; /file1 specifies file1, etc. In the following examples, you can use the above ways of determining file locations where you see file or name.

ls : list directory (folder) contents
mkdir name : make a new directory
rm file : remove (delete) a file. You can use paths (see info for cd) to delete a file in another directory than the current one.
rm -r file : remove a directory and its contents
cd name : choose a directory (open a directory).
cp sourcefile destinationfile : copy a file. You can copy a file from one directory to another, also changing its name, by using paths.
mv sourcefile destinationfile : move a file. This is also a way of changing a file's name.
less file : simple way of looking through a file. Type q to quit, space to move down in the file.
vi file or vim file : text editor (vi or vim) to create a file (if it doesn't exist already) or edit an existing file. Press i to enter edit mode. Press esc to leave edit mode. To save, leave edit mode and type :w . To save and exit, leave edit mode and type :wq or ZZ . To exit without saving, leave edit mode and type :q! .
scp sourcefile destinationfile : secure copy file. Good for copying files to and from a remote cluster. For example, if your username were bob, and you wanted to copy the file trees.nex from the directory /usr/bob/analyses on server.podunk.edu to the directory you are currently using on another computer, you could type scp bob@server.podunk.edu:/usr/bob/analyses/trees.nex trees.nex.
man commandname : open a manual (instructions) for a command.
ssh username@computername.university.edu : connect to a remote host.
top : see which processes (basically, programs) are running, their identifying numbers, and other information. You can kill (force quit) processes from here.

nohup paup -n batchfile > logfile & : starts a paup run in automatic mode immune to hangups (for example, your run will continue on a cluster even if the computer you used to start it from shuts down). 
nohup mb batchfile > logfile & : starts a MrBayes run immune to hangups. Note that the logfile will get very large.
To translate mac line endings to unix line endings, use tr '\015' '\012' < mac.filename > unix.filename
To translate unix line endings to mac line endings, use tr '\012' '\015' < unix.filename > mac.filename


To create batch files for PAUP, see my page for PAUP batch files, and also see PAUP's command reference document, available from PAUP's downloads page.
To create batch files for MrBayes, see this page by Rod Page.


In addition to using ssh to connect to a remote computer, it is sometimes convenient to control a remote computer using its GUI, just as if you were sitting at the screen. One way to do this is to set up the remote computer as a VNC server and then use a VNC client to control the remote computer. I use Mac OS X, so these instructions are for using that operating system (I've tried both 10.2 and 10.3), though VNC in general works on all popular operating systems. Also, the instructions are largely based on a more detailed wiki at Brandeis on configuring VNC for Mac OS X -- I have modified them slightly and put them here for my own reference, and as a hedge against the ephemerality of the web.

First, download OSXvnc on the computer you want to control remotely (the "remote computer"). Put it in the Applications folder. Start OSXvnc. Under General > Passwords, type in a VNC password. Under General, set a display number (typically 0) and a port number (typically 5900). Under Sharing, select the box saying "Allow only local connections (require SSH)" -- this will ensure that only secure (SSH) connections are allowed. Also set up your Startup preferences -- you generally want the VNC server active all the time, I believe. You should also remember your short user name (if in doubt, open the program Terminal (in Applications > Utilities) and look at the text immediately preceding the "%", such as jsmith%) and system password (the password you may use when logging in), which may be different than the password you entered in OSXvnc.

On the remote Mac, go to System Preferences > Sharing > Services. Activate "Remote Login".

Download Chicken of the VNC (or some other VNC client) on the local computer you want to use to access the remote computer.

Open the program Terminal (in Applications > Utilities) on the local computer. Type ssh -Nfn -L localport:127.0.0.1:remoteport shortusername@remotecomputer . For example, if your shortuser name were jsmith,  you wanted to use a localport of 5901,  set up the port in OSXvnc on the remote computer as 5900, and knew the remote computer IP address (easy if the IP address is static (unchanging), or you can use a service like dyndns to maintain a constant hostname (like jsmithhome.dyndns.org) with a constantly updated IP address), you would type ssh -Nfn -L 5901:127.0.0.1:5900 jsmith@jsmithhome.dyndns.org . You would then enter your system password (the one you use on the remote computer to log in).

Then, open Chicken of the VNC on the local computer. In the host field, just type "localhost" [no quotes]. In the port field, type the localport (in the example above, 5901). In password, type the password you entered in OSXvnc (not the system password). On display number, type the local display, probably 0. Connect, and, if all goes well, the remote computer screen will appear in a window on your local computer. You can type, use function keys, use the mouse, etc., normally.

Sometimes, OSXvnc seems to need to be open on the remote computer to establish a connection. If this is so, before using the ssh command above, use ssh shortusername@remotecomputer , then, after logging in, type open /Applications/OSXvnc.app (assuming the program is called OSXvnc and is in the Applications directory) to start it running. Then continue as above.

Finally, when you're done with the connection, close the window in Chicken of the VNC and go back to terminal, hit return a few times, and type logout to disconnect from the remote computer.

Note that it is easier to set up this remote control (not requiring the steps in Terminal, but requiring an additional step in Sharing preferences) if you are willing to allow everything you send over the internet between the computers to be insecure. The approach above (which uses SSH tunnelling) is more secure.