In this exercise (except the first part) you are going to use some data files that should be in this afternoon's working directory. Change to this directory:
cd malignmentYou will find that the directory is empty! The files you need are in the directory "/usr/cbs/phdcourse/malignment". You can copy all of them to your directory with the command
cp /usr/cbs/phdcourse/malignment/* .The "*" means 'all files'. The "." at the end of the line (don't forget it!) means 'current directory'.
Now check that you have the files (there should be seven of them) with the ls command.
Note: The three solutions described on page 3 are only a subset of the distance matrix methods. They all imply a molecular clock and therefore produce rooted trees. This is not the case of the "neighbour joining" algorithm we are going to use in the next part.
Technical note: This sites uses java, a WWW programming language. We sometimes experience problems running it from some of our machines. If you do not see the phylogenetic tree displayed in the center of the intro page, run Netscape from the machine genome instead. Do the following:
Technical note: There is a small bug in the java program, which means that parameter changes are ignored if you just click at the "New Tree" button. To change a parameter: click in the field you want to change, type in the new number, and press ENTER. This goes for all the subsequent pages also.