Phylogenetic footprinting can be improved by unrealistic phylogenetic tree

                   A phylogenetic tree is a kind of branching drawing that can help infer  evolutionary relationship between different organisms. DNA binding motifs are being utilized in doing phylogenetic footprinting. The footprinting requires the knowledge of substitution rates that cannot be calculated easily.

                  Recently Nettling et. al. (2017) have carried out classification performance of phylogenetic footprinting. They calculated substitution rates and found that rates that are near 1 or are very high lead to improved classification performance of phylogenetic footprinting.

                 The phylogenetic footprinting was implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo

Reference:

Nettling M. et. al.(2017) Unrealistic phylogenetic tree may improve phylogenetic footprinting. Bioinformatics 33 (11) 1639-1646.