Below you can find a list of frequently asked questions as well as a list of help topics that are linked from the analysis and results pages. If you don't find all the help you need, please send an e-mail to one of the authors listed on the contact page.
You need Adobe Flash installed for the Cytoscape plug-in.
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. More information can be found here: File Formats
For inter-molecular analysis a second data file can be submitted which contains homologues of a different gene/protein. The sequences in this file do not need to have the same number of species/strains but must have at least some common species/strains.
For a more realistic and informative 3D graphic a PDB structure file can be provided. If the PDB ID is known then the server can retrieve these automatically.
A Newick formatted tree can be submitted. We suggest using a tree calculated using either maximum likelihood or bayesian statistics using RAxML/MrBayes etc. In the case that a tree is not submitted CAPS2.0 will create a distance based tree automatically.
Increasing the bootstrap threshold leads to sites which are coevolving over a greater proportion of the phylogeny. Our advice is that if you wish to discover pairs of coevolving sites which are important for all species/strains in your alignment then this number should be close to 1. If you wish to identify lineage specific coevolution this number should be lower.
This parameter allows the user to remove those columns of the alignment with large numbers of gaps. A value of 1.0 for this parameter will only include columns which have no gaps.
Type error I threshold to detect significant co-evolving sites. Lowering this value will result in fewer false positives but MAY remove true positives.
This parameter defines how many multiple sequence alignments are simulated. We suggest 100 alignments. In the case that the user finds their data does not converge within 100 simulations we suggest using the convergence option (detailed below). Each simulated alignment will have the same number of columns as the input alignment and will be tested using the same method as the real data. This ensures that the data is compared to a null distribution without coevolution pressures.
Using this option will scale BLOSUM scores evolutionary distance. These distances are either those supplied by the user in the phylogenetic tree OR are those JTT distances created when CAPS2 creates a phylogenetic tree for the user.
CAPS searches through all sequences of structures in PDB for a match that has a minimum percentage identity to the reference sequence (90% by default). The best hit at or above the threshold is downloaded and used for the analysis.
If after performing the simulations the distribution drawn has not converged within 0.0001 of the mean, additional similations will be performed until such time as there is convergence. We suggest using this when your data has many assymetries.
If a 3D structure was submitted a table will be included below the Jmol plugin, which allows to select individual groups of co-evolving sites via a radio button.
Each group of co-evolving sites is given a name consisting of incremental numbers.
For each pair of sites in a group that is found within the 3D structure the atomic distance is calculated. The mean of all pairs in a group is shown in the table.
This table column indicates the number of sites that the group of co-evolving sites consists of.
This table column indicates how many of the co-evolving sites are included in the 3D structure. This can be smaller than the overall number of sites if the 3D structure covers only parts of the input sequence.
This table column lists the residue indices associated with the co-evolving sites. These refer to the position of an aminoacid within the reference sequence. Bold numbers indicate residues that are found within the 3D structure.
This table column lists the residues associated with the co-evolving sites. Bold letters indicate residues that are found within the 3D structure.
For more help please feel free to contact the authors (see contact page).