DNA sequences are generated from a rooted or unrooted phylogenetic tree under the substitution model. The branch lengths of the phylogenetic tree are in mutation units, i.e., number of mutations per site. Users are required to upload a tree file (for example, test.tre). If the tree file contains multiple phylogenetic trees, the simulation generates DNA sequences for each tree in the tree file. Users also need to provide values for the parameters (rates, base frequencies, gamma) in the substitution model as well as the sequence length being generated by the simulation. For example the parameter setting for the JC model with the sequence length = 1000 bp is
rate=1,1,1,1,1,1 basefreq=0.25,0.25,0.25,0.25 gamma=0 seqlength=1000
An example input tree file test.tre is available for download. After submission, a unique web link will be generated for users to download the result of the analysis.