Freeware program for construction and bootstrap (and jackknife) analysis of phylogenetic trees from binary data (RAPD, RFLP, AFLP etc.)

Recent windows version  Download here (archive containing 3 files: program, sample data, short manual)

Advantages:

Easy setup (none, just autoextrac and run)

Easy operation (paste your data from spredsheet and press run)

Performs phenetic (UPGMA) and fylogenetic (NJ) analyses

Most universal resampling techniques (bootstrapping, jackknifing, OUT-jackknifing)

All in one (for better presentation of data you will probably need some tree-drawing program, for example Treeview available here)

Authors: Adam Pavlicek and Jaroslav Flegr, Faculty of Sciences, Charles University, Prague, Czech republic

More information on the FreeTree pragram is given in:

Hampl V., Pavlícek A., Flegr J. (2001) Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with a freeware program FreeTree: Application to trichomonad parasites. International Journal of Systematic and Evolutionary Microbiology, 51: 731-735.

The paper is available  here

Another useful program for systematics and molecular systematics Treept(testing correlation between phylogenetic relatedness and phenetic similarity) is available here