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If you are working through a remote server or computer cluster like Perun or Graham, and you are generating alignment files, you may want to check quickly the quality of your alignment. Is there anything strange, are the sites properly aligned, is there perhaps one sequence that is clearly not aligned?
You would typically transfer the alignment file to your local computer so that you can inspect the alignment visually, with SeaView or AliView:
$ rsync <user>@perun.biochem.dal.ca:<alignment_file> .
However, this requires a lot of actions and key strokes: 1. Open a new terminal window 2. Look up the location of the alignment file on the remote file system 3. Decide where you want to have the file on your own file system 4. Invoke the above command 5. Type in your password 6. Open the alignment file with SeaView or AliView 7. Optionally delete the file now that you have seen it
As you might imagine, this is not ideal.
Thankfully, there is a tool available that allows you to view alignment files directly in your terminal, even if they are on a remote system! Alan