论文信息 - Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites

Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites

Motivation: To improve the estimation of evolutionary distances between nucieotide sequences by considering the differences in substitution rates among sites. Results: TREECON for Windows (Van de Peer.Y. and De Wachter.R. Comput. Applic. Biosci., 9, 569-570, 1994) is a software package for the construction and drawing of phylogenetic trees based on distance data computed from nucleic acid and amino acid sequences. For nucleic acids, we here describe the implementation of a recently developed method for estimating evolutionary distances taking into account the substitution rate of individual sites in a sequence alignment. Availability: TREECON for Windows is available on request from the authors. A small fee is asked in order to support the work and to reinvest in new computer hard- and software. More information about the program and substitution rate calibration can be found at URL http://bioc-www.uia.ac.be/uJ yvdp/treeconw. html. Contact: E-mail: yvdp@uia.ua.ac.be

Yves Van de Peer | Rupert De Wachter | Y. Peer | R. Wachter

[1] A Gajdos,et al. [Evolution of protein molecules. I. Protein synthesis]. , 1972, La Nouvelle presse medicale.

[2] L. Jin,et al. Limitations of the evolutionary parsimony method of phylogenetic analysis. , 1990, Molecular biology and evolution.

[3] Y Van de Peer,et al. The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. , 1996, Journal of molecular evolution.

[4] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[5] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[6] G. Olsen,et al. Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. , 1987, Cold Spring Harbor symposia on quantitative biology.

[7] J. Felsenstein. CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[8] Yves Van de Peer,et al. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment , 1994, Comput. Appl. Biosci..