SEMPHY is a tool for data-intensive phylogenetic reconstruction. It infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree.
SEMPHY searches for both the most likely topology of the evolutionary tree, and the optimal lengths of its branches. It uses the algorithmic paradigm of Structural EM in a new computational method for phylogenetic inference, making computation both effective and efficient: SEMPHY can handle very large data sets with both good accuracy and reasonable running time. We will refer to the EM procedure as the "SEMPHY step".

All uses of SEMPHY are by calling the executable semphy from a command prompt with some parameters: semphy [parameters...]

The license of this software is Freeware, you can free download and free use this calculator software.