Abstract: Much effort has been devoted to the detection, from multiple sequence alignments of homologous proteins, of pairs or groups of amino acid positions that evolve in a nonindependent – or compensatory – manner. It is expected that such clusters of positions might either tend either to be proximal in the mature, folded protein, or to be involved in similar aspects of protein function. Several such methods have been shown to be reasonably effective in the detection of intra-protein contacts. However, all of the most successful published algorithms rely on pairwise comparisons between aligned sequences. We wished to investigate whether evolutionary information (the topology and branchlengths of the phylogenetic tree describing relationships between the sequences under study) can allow an improvement in the prediction of intra protein contacts from correlated substitutions.