Bellow is a list computational tools developed for (1) classification of nucleic acid / protein sequences and (2) identification and characterisation of nucleic acid secondary strucutres within virus genomes

1. Sequence Demarcation Tool version 1.2 (SDTv1.2): A program designed for objective creation of dataset based on sequences pairwise to suite downstream analyses is availble from http://web.cbio.uct.ac.za/SDT

==> The source code can be downlaoded from the following link SDTv1.2 source code
2. Nucleic Acid Predictor (NASP) is avaible from http://web.cbio.uct.ac.za/~yves/nasp/

3. Scripts for inference and analysis for signals of natural selection and coevolution:

• Purifying Selection Analysis - Tajima - Fu and Li based permutation Test ☞instructions
Download Scripts for Tajima - Fu and Li based permuation test
• Synonymous Substitutions Analysis - PARRIS-FUBAR ☞ instructions
Download Scripts that run GARD, PARRIS and FUBAR
Downlaod Scripts that compare dS rates between paired and upaired sites
• Complementary Coevolution Analysis ☞instructions
Download Scripts used to prepare input alignments and pythologenetic trees
Download Scripts used to run the complementary coevolution script
Download Scripts used to test for association between complementarily coevolving sites and paired sites
4. Nucleic Acid Visualisation and Analysis (NAVA) used for a computer program Nucleic Acid Visualisation and Analysis (NAVA) that permits ranking structures of based on of structure conservation, natural selection and coevolution evidence, and visualisation of individual structure with the selection information overlaid is avaible from https://sites.google.com/site/cbiomichael/software

5. StructureMap: a program that draws a genome map marking locations of secondary structures for comparative purposes ☞instructions
Download StructureMap
==> The source code can be downlaoded from the following link StructureMap source code
6. SelectionMap: a program used for visualisation of selection data☞instructions
Download SelectionMap-v1.0
==> The source code can be downlaoded from the following link SelectionMap source code
7. A module implemented Recombinatio Detection Program (RDP) allows testing for avoidance of nucleic acid fold disruption following genetic recombination. It can be obtained from the following version of RDP ...

Written by Brejnev Muhire
Computational 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: mhrbre001@myuct.ac.za or mubrejnev@gmail.com