The user needs to upload a file with aligned DNA or protein sequences in Fasta, Mega or sequential Phylip format that represent homologues of the same protein/gene from different organisms.
For inter-molecular analysis a second data file can be submitted which contains homologues of a different gene/progein. The sequences in this file need to be of the same type and order, and need to contain the same number of sequences.
For a more realistic and informative 3-D graphic a PDB structure file can be provided. If the PDB ID is known then the server can retrieve these automatically.
This lets the user specify the method used to identify the important or significant sites.
Type error I threshold to detect significant co-evolving sites.
The number of pseudo-replicates to generate the random distribution for the significance analysis.
The minimum R-value to detect a pair of co-evolving sites.
How to weigh correlation by the divergence time between sequences.
Parameter to determine the weight of gaps in the detection of co-evolving sites.
The minimum value for the correlation coeficient to be considered for filtering.
The maximum number of sites in a group of co-evolving sites permitted, given in percentage of protein length.
For more help please feel free to contact the authors (see contact page).