These must be done by hand or through the use of additional programs like, e.g. Clustal or TreeAlign . Using the programs When run, each program will display on your terminal a screen containing the program role and version and a menu. Yes, at seq. To change any option type the letter at the left of its line in the menu. You will be prompted for additional information as needed.
Penny finds all most parsimonious trees applying a branch and bound search strategy.
You should rename these files if you want to preserve the results, otherwise they will be overwritten by the next program you run. Usually it contains the name of the program, the input data and the phylogenies plus associated information. Note that in most cases produced trees are unrooted . This file can then be printed on the appropriate device. In general you should always do a bootstrap analysis to assert the significance of the results of your phylogenetic analysis.