This is a server that provides rate shift analyses for proteins. It takes a number of aligned proteins as input. The two families to be analysed should be inserted in the first and second text areas. The outgroup sequences should be inserted in the last text area. All the sequences should be part of one big alignment, and should be inserted in fasta format. If a phylogeny is input, it should be in the newick format. The algorithm is described in the reference below. Comments are very much appreciated. At the moment, the server has a maximum of 45 sequences in each family and 10 sequences in the outgroup. The maximum alignment length is 600. Bjarne Knudsen (bk@daimi.au.dk)
When you press `Calculate' your data will be processed. If an outgroup is not specified, the root is used as the split point between the two families, if it is binary, does indeed split the tree into the appropriate sub-families and branch length optimization is not chosen. Otherwise, the root of the tree is put in the center of the branch connecting the two families.
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