How to work on ClustalMU:

ClustalMU is on persy.aules.upf.edu server. If you want to take a look on ClustalMU you can download it by clicking on that link.

Steps after downloading:

1) This program is compressed with tar. To obtain the full package write:

tar xvfz clustalmu.tar.gz

That will create a folder inside which you will find the files clustalmu.pl, funcions.pm, blossum30.mat, blossum45.mat, blossum62.mat, blossum80.mat, continc4seq.txt, continc5seq.txt and continc6seq.txt.

2) Running the program:

While in a terminal console, you have to be in the folder where you have opened the tar file. Call the program by typping:

./clustalmu.pl FASTAFILE Substitution Matrix GOP GEP

Where FASTAFILE can be continc4seq.txt, continc5seq.txt or continc6seq.txt (or a FASTAFILE containing your sequences); Substitution Matrix can be blossum30.mat and so on (if you want to use a PAM matrix you have to ensure that its format is the same as in blossum matrix); GOP (Gap Open Penalty) should be -2 (you can write the gap penalty at your will) and finally GEP (Gap Extended Penalty) which should be less than GOP (it has to be more in GOP because it is less parsimonious to open three gaps than to open one gap and extend it two positions).

3) Results:

Results are obtained as an outfile.txt. In that outfile you find the first distance matrix obtained from the pairwaise alignment, and the tree guide, from which the progressive alignment should be done.



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