The Win95/98/NT program FreeTree for computation of distance matrices and 
construction of phylogenetic or phenetic trees on the basis of random amplified 
polymorphic DNA (RAPD), RFLP and allozyme data is presented. In contrast to 
other similar software, the program FreeTree (available at 
http://www.natur.cuni.cz/~flegr/programs/freetree or 
http://ijs.sgmjournals.org/content/vol51/issue3/) can also assess the robustness 
of the tree topology by bootstrap, jackknife or operational taxonomic 
unit-jackknife analysis. Moreover, the program can be also used for the analysis 
of data obtained in several independent experiments performed with non-identical 
subsets of taxa. The function of the program was demonstrated by an analysis of 
RAPD data from 42 strains of 10 species of trichomonads. On the phylogenetic 
tree constructed using FreeTree, the high bootstrap values and short terminal 
branches for the Tritrichomonas foetus/suis 14-strain branch suggested 
relatively recent and probably clonal radiation of this species. At the same 
time, the relatively lower bootstrap values and long terminal branches for the 
Trichomonas vaginalis 20-strain branch suggested more ancient radiation of this 
species and the possible existence of genetic recombination (sexual 
reproduction) in this human pathogen. The low bootstrap values and the star-like 
topology of the whole Trichomonadidae tree confirm that the RAPD method is not 
suitable for phylogenetic analysis of protozoa at the level of higher taxa. It 
is proposed that the repeated bootstrap analysis should be an obligatory part of 
any RAPD study. It makes it possible to assess the reliability of the tree 
obtained and to adjust the amount of collected data (the number of random 
primers) to the amount of phylogenetic signals in the RAPD data of the taxon 
analysed. The FreeTree program makes such analysis possible.