STEM (Species Tree Estimation using Maximum) is is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model. The program will either return the exact ML tree computed using the methodology of Liu and Pearl (2008; see also Roch and Mossel, 2008), compute the likelihood for a user-specified tree, or search for a set of highest likelihood trees. The method for searching the space of trees is a simulated annealing algorithm and is described in the reference above (with more detail given in Salter and Pearl, 2001).

STEM requires several input files. The first of these is the file which gives the information for the gene trees, which must be called genetrees.tre. This file contains the gene trees with branch lengths in Newick format. Gene trees must be rooted and must satisfy the molecular clock, although the program won't check for this (you will likely get an error or it will run indefinitely if this it not the case). Directly in front of each gene tree is a number within square brackets that gives the rate multiplier for each gene (this allows each gene to evolve at its own rate - see the paper above for details).

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