Sequence Demarcation Tool Version 1.2 (SDTv1.2) is a free and easy to use program that allows classification of virus sequences based on sequence pairwise identity. It takes as input a FASTA file of aligned or unaligned DNA or protein sequences and aligns every unique pair of sequences, calculates pairwise similarity scores, and displays a colour coded matrix of these scores. It also produces both a plot of these pairwise identity scores and text files containing analysis results. The identity scores are calculated as 1-(M/N) where M is the number of mismatching nucleotides and N the total number of positions along the alignment at which neither sequence has a gap character.
1. Mastrevirus reference sequences alignment mastrevirus_references.fas (last updated 20/11/2012) 2. Mastrevirus reference sdt file mastrevirus_references.sdt (last updated 20/11/2012)
This a command-line version of SDTv1.0 written in Python, which runs on Linux and Mac OSX, 32 and 64 bit operating systems ).
SDTMPI_Linux (32 and 64 bit) is a free Linux-based Python program that uses a parallel programming library for Python (mpi4py) to allow quick calculations of DNA sequence pairwise similarities for large numbers of sequences that cannot be practically analysed using SDT Version1.0 (for example above 1000 or more sequences). Given a FASTA file containing DNA sequences, the program aligns all possible pairs of sequences using Muscle, ClustalW2, or Mafft, calculates the sequence similarity score for each pair and uses a rooted neighbour joining phylogenetic tree to cluster closely related sequences based on similarity scores. It outputs a text file containing the scores and a ".sdt" file that can be open with SDTv.1.0 Windows version to easily visualise the pairwise identity distribution plot and colour coded similarity matrix. The indentity scores are calculated as 1-(M/N) where M is the number of mismatching nucleotides and N is the total number of positions along the alignment where neither sequence has a gap character.
Please cite:Muhire BM, Varsani A, Martin DP (2014) SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation. PLoS ONE 9(9): e108277. doi:10.1371/journal.pone.0108277
Written by Brejnev MuhireComputational Biology Group - University of Cape Town Institute of Infenctious Diseases and Molecular Medicine (IIDMM) Anzio Road Observatory 7925 Cape Town South Africa Tel: +27 21 406 6058/6176 Fax: +27 21 406 6068 Email: firstname.lastname@example.org or email@example.com