PAUP* advice from David Swafford:

-------------------------

Things that you would examine with your own analyses:

The information that you really want from the program are the best trees found in each search replicate and the globally best across all replicates. After each individual replicate finishes, the best trees from all of the replicates completed thus far are written to the .best.all.tre file. When all replicates have finished, the best tree across all replicates is written to the .best.tre file.

The config files used here are set up to use a feature of the program that collapses internal branches that have an MLE length of zero. This may result in final trees that have polytomies. This is generally the behavior that one would want. Note that the likelihoods of the trees will be identical whether or not the branches are collapsed.

When the two search replicates have completed, we can more closely examine the results.

First, take a look at the end of the .screen.log file. You will see a report of the scores of the final tree from each search replicate, an indication of whether they are the same topology, and a table comparing the parameter values estimated on each final tree.

There are two possibilities:

1. The search replicates found the same best tree. You should see essentially identical lnL values and parameter estimates. The screen.log file should indicate that the trees are identical.
2. The search replicates found two different trees. This is almost certainly because one or both were trapped in local topological optima. You will notice that the lnL values are somewhat different and the parameter estimates will be similar but not identical. The search settings may influence whether searches are entrapped in local optima, but generally the default settings are appropriate.

We can also evaluate and compare the results of our two search replicates in PAUP*. Being able to open the results of one program in another for further analysis is a good skill to have.