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sdt website  

SDT 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.

Required Modules


  • sdt

System Variables

  • HPC_SDT_DIR - installation directory


If you publish research that uses sdt you have to cite it as follows:

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