SelectionMap SelectionMap is a free Windows computer program designed to detect and graphically illustrate the types and degree of natural selection acting along gene alignment(s). In addition the program allows comparison of natural selection patterns between two or three alignments of homologous genes. The program can either take as input codon alignment(s) in FASTA format for detection of selection and plotting of the selection map, or it can take as input the output files generated by the selection detection methods FUBAR (Murrell et al. 2013) and/or MEME (Murrell et al. 2012). The program detects selection using the FUBAR method implemented in HYPHY (Pond et al. 2005) and then produces a selection map in which every codon site is represented by a vertical bar with a colour and height respectively indicating the type and strength of selection acting at that codon. In general, when gene alignments of related species are loaded, the figure that is produced indicates sites that are evolving under: (1) negative selection favouring the same amino acid in the different species; (2) negative selection favouring different amino acids in the different species; (3) negative selection in only one of the species; (4) positive selection; and (5) episodic positive selection.
Click here to download SelectionMap-v1.0 the most up to date version; instructions (uploaded on 28/April/2016). For help please visit and post your error on the SMap forum Report any bug to mhrbre001@myuct.ac.za or mubrejnev@gmail.com
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: mhrbre001@myuct.ac.za or mubrejnev@gmail.com