The term Phylogentics is the study of evolutionary relationship between different species, organisms or genes. These relationships are depicted as branched, tree like diagrams that provide insight into the events that occurred during the evolution process. These trees may also have a root which is known as the common ancestor. Building the "Tree of Life" has been the prime objective of many researchers, until it was proved that the tree of life cannot be represented by a single? tree. Many evolutionary events cannot be represented with the help of a simple tree, hence phylogenetic networks came into picture. Phylogenetic networks can be classified into different categories. In this paper, an algorithm (ReTF) has been proposed which would improve the results of the current phylogenetic network reconstruction algorithms. The idea behind ReTF is rearranging the input sequences in a way that the new arrangement gives a better tree, since the order of input sequences affects the outcomes of phylogenetic network. © 2013 IEEE.