GRaphical footprint based Alignment-Free method (GRAFree)

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GRAFree (GRaphical footprint based Alignment-Free method) is a python based program for deriving the phylogenetic tree from the genomic sequence data of different species based on the graphical representation of the sequences. Important features of this method is summarized below.

• It plots the genome sequences in a two dimensional coordinate plane by considering successive shifts in x and y coordinates using three different encodings of DNA alphabets.
• Computes the drifts from the 2D representations. Represents each drifts by a 5-dimensional feature vector which further fragments for better resolution.
• Apply a novel distance function to compute the pairwise distance matrix from the 5D feature vector. Apply the UPGMA to derive the phylogenetic tree from the distance matrix.
• This program generates bootstrap sequences by considering the probability of variances of the genomic sequences and generates the bootstrap trees from the bootstrap sequences.
• Additionally, this program gives the composition of the genome sequences such as, lenght of sequence, fraction of A, T, G, and C, AT shew and GC skew.

Download executable (version 1.0)

GRAFree.zip

For any queries, please contact:

• Aritra Mahapatra
  Department of Computer Science and Engineering
  Indian Institute of Technology Kharagpur
  Email: aritra DOT mhp AT iitkgp DOT ac DOT in
• Jayanta Mukherjee
  Department of Computer Science and Engineering
  Indian Institute of Technology Kharagpur
  Email: jay AT cse DOT iitkgp DOT ac DOT in