Comparison of several applications for comparison of protein sequences.

The table compiles the name under which a method is most often referred to, the type of evolutionary method it captures, and the references for the original (method) publication, as well as for the accompanying database and/or server publications, where applicable. “Variability” stands for the “degree of variability.” The table is not an exhaustive overview of the field, but, rather, illustrates the following. (i) Bioinformatics applications are usually presented as an algorithm and its application (third column), sometimes as a database of pre-calculated results, and sometimes as a server. Cube, described in this work, is a server. (ii) Furthermore, as of this writing, Cube is unique in that it provides a heuristic scoring both for the overall degree of variability, and for the type I and type II divergence. (iii) Type I divergence does seem to have the thinnest coverage in the literature, and is tackled by Cube.
1http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl.