Help comparing cladograms

[DaveB]

I am comparing the protein sequences of several proteins for several different animals. I have selected the proteins and the animals and I retrieved the protein sequences. I ran them through the ClustalW program and obtainted distance matrices that show the distance between each organism based on a given protein sequence. ClustalW also outputs a cladogram showing the relationships between each of the organisms. I have a couple of questions.

1) How can I meaningfully compare the cladograms? They are not identical, which shows that the proteins have evolved differently. If the proteins were all the same for the different organisms or if the changes were equivalent in some way, the the cladograms would be the same. Since they are different , who do I interpret and discuss this?

2) I am not sure exactly what the distance measure is or how it is calculated. I have checked the ClustalW documentation but I cannot really see any reference to how the distance matrix is calculated.

My plan is to compare the cladograms, which show the relationship among the organisms based on the differences in protein sequence, with their places in the standard taxonomy of Phylum, Class, Order, etc.

thanks

Dave

[Guest]

Dave:

This site may be of help with ClustalW analysis.

http://202.141.140.72/~whotdr/0501_phylo.htm

Matt M