Treept

Freeware program for testing correlation between phylogenetic relatedness and phenetic similarity using permutation test.

The program can by used also for several simple statistical tests – permutation analogy of t-test, ANOVA and linear regression.

The present version of the program can analyze (t-test, ANOVA, regression) also contaminated data, e.g., the data in which some cases in the group 1 should be in fact in the group 2.

Recent version of the program Download here (zip archive containing program, sample data, short manual etc.)

Advantages:

Excellent program, no other freeware programs for testing correlation phenetic traits with genetic or phylogenetic relatedness or for statistical analysis of contaminated data are available.

Examples of problems to be solved with TREEPT

  1. Have genetically related strains of a parasite also a similar virulence?
  2. Do phylogenetically related species live in near areas

Authors:

Pavel Zaboj and Jaroslav Flegr, Faculty of Sciences, Charles University, Prague, Czech republic

More information on the Treept pragram is given in:

Flegr J., Záboj P. and Vanácová Š. (1998) Correlation between aerobic and anaerobic resistance to metronidazole in trichomonads:  Application of a new computer program for permutation tests. Parasitology Research, 84: 590-592. » PDF

and

Flegr J. and Záboj P. (1997) PTPT, the freeware program for permutation testing concordance between phylogeny and the distribution of phenetic traits.  Acta Soc. Zool. Bohem. 61: 91-95. » PDF

The analysis of contaminated data is described in:

Flegr J. Havlíček J. (1999) Changes in personality profile of young women with latent toxoplasmosis. Folia Parasitologica, 46: 22-28.  » PDF

Another useful program for systematics and molecular systematics FreeTree (construction and bootstrap (and jackknife) analysis of phylogenetic trees from binary data) is available here

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