Right answer is (d) The user does not necessarily provides a phylogenetic tree that defines the evolutionary relationship of the input sequences
Easiest explanation: The user also needs to provide a phylogenetic tree that defines the evolutionary relationship of the input sequences. One may obtain the tree information from the “Tree of Life” web site, which archives known phylogenetic trees using ribosomal RNAs as gene markers. It identifies unusually well-conserved motifs across a set of orthologous sequences.