Print the results to the screen and/or a file The simplest way to print the results of a likelihood maximization step is simply to print the likelihood function: fprintf(stdout,theLikFun); This C-like command prints the structure theLikFun to the default output device stdout (stdout is typically the screen). The results of this statement are the following: Log Likelihood = -589.252801936419; Tree myTree=((a:0.0320567,b:0.00598813)Node1:0.045548,c:0.0257871,d:0.0769886); When asked to print a likelihood function, Hy-Phy first reports the value of the likelihood function. It follows with a listing of all estimated parameters. Any parameters associated with particular branches in a tree are reported in a tree-like description, as shown in the output above. Each of the branches in the unrooted phylogeny has an associated "branch length"; branch lengths are defined as ``the expected number of nucleotide substitutions per site''. Those values appear after the colon following the label for each branch. For example, the estimated branch length leading to the node "b" is 0.00598813. Note that the internal node in the tree has been automatically named ``Node1'' by Hy-Phy and its associated branch length is 0.045548. We will see many examples of this type output in the later examples. Hy-Phy also allows for more detailed user control of printed output, using a C-like fprintf syntax. The later examples will illustrate this functionality.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002