A Practical Manual for Real-World Phylogenetic Systematic Methods
As of 4-26-16

Handling large data sets

Creating a simple data matrix using TnT.

Performing a True Phylogenetic Analysis using TnT.: Finding the most parsimonious tree

Viewing the Results

Calculating Consensus

Trouble-shooting:

Things I have come across:

This concludes our introductory demo. There is, of course, much much more to phylogenetic analysis, but now you should be able to explore it on your own. If you have digested the information here, you can perform a competent phylogenetic analysis.

Congratulations, cladist.