Simprot Web Interface: Simprot v1.0 is a program that simulates protein evolution by substitution, insertion and deletion. It is based on the paper
Pang, A, Smith A, Nuin PAS, and Tillier, ERM 2005. Simprot: using an empirically determined indel distribution in simulations of protein evolution. BMC Bionformatics, 6:236.
Simprot v1.0 was born as a command line tool for Linux and now has been develpped for different systems. A new graphical version for Linux and Windows has been released and can be donwloaded here (not available at the moment). And this web interface is available to run the simulations, having the same functionality of the standalone programs.
Simprot uses as input file a bifurcating phylogenetic tree (Newick, usually extensions .TRE or .TREES or no extension at all). To run Simprot select your tree file below by clicking on Browse, adjust the parameters at your will and click on Run Simprot to start the simulation.The result will be displayed in a text box and can be saved by clicking on the links. At the moment two files are written: a sequences FASTA file and an alignment FASTA file.
This service is currently not available at this webpage, please click here to use the webserver. Sorry for any inconvenience.
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