Likelihood estimation of model parameters made easy. MLtree implement maximum likelihood estimation of model parameters given a fixed topology with user-defined branch lengths. It includes DNA model of substitution as well as a serie of Markov model designed for 2-states characters.

Usage: mltree -f filename -m model -t ntaxa -d ndata [-e] [-n] [-p np param1 param2 ...] [-s scalebrlen] [-o ming|newton|uphill] [-h] [-r num]

where:
-f = file name containing the tree description
-t ntaxa = number of taxa
-d ndata = number of data characters per taxa
-m model = which model to use (Mk1, Assym2p, CO2, F81, F84, HKY85, TN93, GTR)
-e = use equal state frequencies
-n = normalize transition matrix
-p np param = np is the number of parameters to set, and param are there values
-s = scale branch length
-o = optimization method, by default, ming is done
-h = test character assignement at each node (see Pagel, 1999)
-r num = randomize observed data num times

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